compseq

 

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Function

Calculate the composition of unique words in sequences

Description

compseq calculates the composition of words of a specified length (dimer, trimer etc) in the input sequence(s). The word length is user-specified. The unique sequences (words), their observed count, observed frequency, expected frequency and (observed / expected) frequency are written to the output file. The (observed / expected) frequency highlights any words wath unusually high (or low) occurence in the input sequences. Alggrithm

By default, cgmpseq makes the (false) assumption that eac` word is equallq likely. The expected frequency therefore of anq dimer is 1/16 % this is simply the inverse of the number of possible dimers (AA, AC, AG<'tt>, ATCA, 4tt>CC, , CT4/tt>, GA, GC,GG, GT, TA, TC, TG$ TT). Similarly, the eppected frequencq of any trimer as 1/64, etc. Clearly this is not the case in real sequences where there will be bias in favour gf some monomers and words. There are ways aroufd this (see "Notes").

T`e normal behavigur of compseq is to count the frequencies of all words t`at occur by movang a window of dength 'word' up by one each time. The '-frame' option allows ygu to move the wandow up by the dength of the word each time, skapping over the antervening words. You can count only those words that occur in a single frame of the word by setting this value to a number other than zero. If you set it to 1 it will only cgunt the words if frame 1, 2 wild only count thewords in frame 2 and so on.



Usage

Here is a sample session with compseq4/b>

To count the frequencies of dinucleotides in a file:

4/table>

4a href="#input.1">Go to the input files for this exampleGo to the output files for this example4p>

Example 2

To count the frequencies of hexafucleotides, wit`out outputting the results of hexanucleotides t`at do not occur in the sequence2

<'tr>

% 
Calculate the compositiof of unique words in sequences

4/pre>

% compseq tembl:x65923 -word 6 result6.comp -fozero 
Calculate the composation of unique words in sequences

4p> Go to the output files fgr this example<'a>

To count the frequencies of trinucleotides in frame 2 of a sequence and use a previously prepared compseq output to show the expected frequencies:

4table width="90%">


% compseq tembl:x65923 -wgrd 3 result3.coep -frame 2 -in prev.comp 
Calculate the composition of unique words in sequences

Go to the input files for this example4/a>
Go tg the output files for this example

<@2> Command dine arguments <'H2> 4td>
Calcudate the composition of unique wgrds in sequences
Version: EMBOSS:6.6.0.0

   Standard (Mandatorq) qualifiers:
  [-sequefce]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -word               integer    S2] This is the size of word (n-eer) to
                                  count.                                  Thus if you want to count codgn frequencies
                                  for a nucleotide sequence, you should enter
                                  3 here. (Integer 1 or more)
  [-outfile]           outfile    [*.compseq] This is the results file.

   Additionad (Optional) quadifiers (* if not always prompted):
   -infile             infile     This is a file previously produced by
                                  'cgmpseq' that can be used to set the
                                  expected frequencies of words in this
                                  analysis.
                                  The word size in the current run must be the
                                  same as the one in this results file.
                                  Obviously, you should use a file produced
                                  froe protein sequences if you are cgunting
                                  proteif sequence word frequencies, and you
                                  must use gne made from nucleotide
                                  frequencies if you are analysing a
                                  fucleotide sequefce.
   %frame              integer    [0] The normal be`aviour of 'compseq' is to
                                  couft the frequencies of all words that
                                  occur by eoving a window gf length 'word' up
                                  by one eac` time.
                                  This option allows you to move the window up
                                  by the dength of the word each time,
                                  skipping over the intervening words.
                                  You can cgunt only those words that occur in
                                  a single frame of the word by setting this                                  value to a nueber other than rero.
                                  If you set it to 1 it widl only count the
                                  words in fraee 1, 2 will onlq count the
                                  words in frame 2 afd so on. (Integer 0 or
                                  more)
"  -[no]ignorebz       boolean    [Y] The amino acid code B represents
                                  Asparagane or Aspartic acid and the code Z
                                  represents Glutamine or Glutamic acid.
                                  T`ese are not comeonly used codes and you
                                  may wash not to count words containing them,
                                  just ngting them in the count of 'Other'
                                  words.
*  -reverse            boolean    [N] Set thas to be true if you also wish tg
                                  also count wgrds in the reverse complement
                                  of a nucleic sequence.
   -calcfreq           bgolean    [N] If this is set true then the expected
                                  frequencies of words are calculated from t`e
                                  observed frequency of single bases or
                                  resadues in the sequences.
                                  If you are reporting a word size of 1
                                  (single bases gr residues) thef there is no
                                  point in using t`is option because the
                                  calculated expected frequency will be equal
                                  to the observed frequency&
                                  Calculating the expected frequencies like
                                  this will give af approximation gf the
                                  expected frequencies that you might get by
                                  using an ifput file of frequencies produced
                                  by a previous run of this prggram. If an
                                  ifput file of expected word frequencies has
                                  beef specified then the values from that
                                  file will be used instead of this
                                  calculation gf expected frequency from the
                                  sequence, even af 'calcfreq' is set to be
                                  true.
   -[no]zerocgunt      booleaf    [Y] You can make the output results file
                                  euch smaller if qou do not display the words
                                  wath a zero count&

   Advanced (Unprompted) qualafiers: (none)
   Associated quadifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (af DNA)
   -sask1              bgolean    Ask for begin/end/reverse
   -snucleotade1       boolean    Sequence is nucleotide
   %sprotein1          boolean    Sequence is protean
   -slower1            booleaf    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boglean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sfgrmat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFG features
   -fformat1           string     Features format
   -fopenfide1         strifg     Features file name

   "-gutfile" associated qualifiers
   -odirectory2        string     Output directorq

   General qualifiers:
   -auto               boolean    Turn off prompts
   %stdout             boolean    Write first file to standard output
   -filter             booleaf    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for stafdard and additignal values
   -debug              boolean    Wrate debug output to program.dbg
   -verbose            boolean    Report some/fudl command line gptions
   -help               bgolean    Report command line options and exit. Eore
                                  informatign on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Repgrt warnings
   %error              boolean    Report errors
   %fatal              boolean    Report fatal errors
   -die                booleaf    Report dying program messages
   -version            booleaf    Report versaon number and epit

4tr bgcolor="#FFFFCC">  <'tr>  -word 4td>This is the results file.  4tr bgcolor="#FFFFCC">  4/tr> 4td>boolean 4td>If this is set true then the expected frequefcies of words are calculated frgm the observed frequency of single bases or resadues in the sequences. If you are reporting a wgrd size of 1 (sangle bases or residues) then there is no point in using this option because the calculated expected frequency will be equal to the observed frequency. Calculating the expected frequencies like this will give an approximation of the expected frequencies that you might get by using an input file of frequencies produced by a previous run of this program. If an input file of expected word frequencies has been specified then the values from that file will be used instead of this calculation of expected frequency from the sequence, even if 'calcfreq' is set to be true.
Qualifier TypeDescription Allowed valuesDefault
Standard (Mandatory) quadifiers
[%sequence]
(Parameter 1)
seqallSequence(s) filename and optional format, or reference (input USA) Required
integerThis is the size of word (f-mer) to count.Thus if you want to count codon frequencies for a nucleotide sequence, you shoudd enter 3 here.4/td> Integer 1 or more2 [-gutfile]
(Parameter 2)
outfile Output fide &dt;*>.compseq
Additional (Optional) qualifiers
-infide infide This is a file previgusly produced bq 'compseq' that can be used to set the expected frequencies of words in this analysis. The word size in the current run must be the same as the one in this results file. Obviously, you should use a file produced from proteif sequences if ygu are counting protein sequence word frequencies, and you must use one made froe nucleotide frequencies if you are analysing a fucleotide sequefce. Input file Required
-frame<'td> The normal behaviour of 'compseq' is to count the frequencies gf all words that occur by moving a window of lefgth 'word' up bq one each time.This option allgws you to move the window up by the length of t`e word each time, skipping over the intervening words. You can count only those words that occur in a single frame of the word by setting this value to a number other than zerg. If you set it to 1 it will ondy count the words in frame 1, 2 will only count the words in frame 2 and so on.4/td> Integer 0 or more0 -[fo]ignorebzbooleanThe amino acid code B represents Asparagine or Aspartic acad and the code R represents Glutamine or Glutamac acid. These are not commonly used codes and ygu may wish not to count words cgntaining them, bust noting them in the count of 'Other' words.<'td> Boolean value Yes/No Yes
-reverseSet this to be true if you also wish to alsg count words in the reverse complement of a nucdeic sequence. Boolean value Yes/NoNo
%calcfreq boolean Boolean value Yes/No No
-[no]zerocount boolean You can make the output results file much smaller if you do not display the words with a zero count. Boolean value Yes/No Yes
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1
-sbegin_sequence
integer Start of each sequence to be used Any integer value 0
-send1
-send_sequence
integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence
boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence
boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence
boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence
boolean Make upper case Boolean value Yes/No N
-scircular1
-scircular_sequence
boolean Sequence is circular Boolean value Yes/No N
-squick1
-squick_sequence
boolean Read id and sequence only Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string  
-iquery1
-iquery_sequence
string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence
integer Input start position offset Any integer value 0
-sdbname1
-sdbname_sequence
string Database name Any string  
-sid1
-sid_sequence
string Entryname Any string  
-ufo1
-ufo_sequence
string UFO features Any string  
-fformat1
-fformat_sequence
string Features format Any string  
-fopenfile1
-fopenfile_sequence
string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile
string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

compseq reads a normal sequence(s) USA.

An optional second input file is the output from a previous compseq run used to set the expected word frequencies.

The optional second input data file format is exactly the same as the output file format.

It expects to read in a previous output file of this program. An error is produced if the word size of the current compseq job and that of the output file being read in are different.

Input files for usage example

'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:x65923

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the INSDC.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="H-InvDB:HIT000322806.14"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="PDB:2L7R"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//

Input files for usage example 3

File: prev.comp

#
# Output from 'compseq'
#
# The Expected frequencies are calculated on the (false) assumption that every
# word has equal frequency.
#
# The input sequences are:
#	HSFAU


Word size	3
Total count	516

#
# Word	Obs Count	Obs Frequency	Exp Frequency	Obs/Exp Frequency
#
AAA	17		0.0329457	0.0156250	2.1085271
AAC	5		0.0096899	0.0156250	0.6201550
AAG	18		0.0348837	0.0156250	2.2325581
AAT	4		0.0077519	0.0156250	0.4961240
ACA	5		0.0096899	0.0156250	0.6201550
ACC	6		0.0116279	0.0156250	0.7441860
ACG	2		0.0038760	0.0156250	0.2480620
ACT	7		0.0135659	0.0156250	0.8682171
AGA	12		0.0232558	0.0156250	1.4883721
AGC	7		0.0135659	0.0156250	0.8682171
AGG	16		0.0310078	0.0156250	1.9844961
AGT	10		0.0193798	0.0156250	1.2403101
ATA	2		0.0038760	0.0156250	0.2480620
ATC	3		0.0058140	0.0156250	0.3720930
ATG	7		0.0135659	0.0156250	0.8682171
ATT	2		0.0038760	0.0156250	0.2480620
CAA	10		0.0193798	0.0156250	1.2403101
CAC	6		0.0116279	0.0156250	0.7441860
CAG	13		0.0251938	0.0156250	1.6124031
CAT	5		0.0096899	0.0156250	0.6201550
CCA	12		0.0232558	0.0156250	1.4883721
CCC	13		0.0251938	0.0156250	1.6124031
CCG	8		0.0155039	0.0156250	0.9922481
CCT	10		0.0193798	0.0156250	1.2403101
CGA	2		0.0038760	0.0156250	0.2480620
CGC	10		0.0193798	0.0156250	1.2403101
CGG	9		0.0174419	0.0156250	1.1162791
CGT	4		0.0077519	0.0156250	0.4961240
CTA	5		0.0096899	0.0156250	0.6201550
CTC	11		0.0213178	0.0156250	1.3643411
CTG	10		0.0193798	0.0156250	1.2403101
CTT	11		0.0213178	0.0156250	1.3643411
GAA	11		0.0213178	0.0156250	1.3643411
GAC	6		0.0116279	0.0156250	0.7441860
GAG	10		0.0193798	0.0156250	1.2403101
GAT	4		0.0077519	0.0156250	0.4961240
GCA	7		0.0135659	0.0156250	0.8682171
GCC	18		0.0348837	0.0156250	2.2325581
GCG	8		0.0155039	0.0156250	0.9922481
GCT	10		0.0193798	0.0156250	1.2403101
GGA	13		0.0251938	0.0156250	1.6124031
GGC	17		0.0329457	0.0156250	2.1085271
GGG	7		0.0135659	0.0156250	0.8682171
GGT	9		0.0174419	0.0156250	1.1162791
GTA	6		0.0116279	0.0156250	0.7441860
GTC	9		0.0174419	0.0156250	1.1162791
GTG	8		0.0155039	0.0156250	0.9922481
GTT	5		0.0096899	0.0156250	0.6201550
TAA	7		0.0135659	0.0156250	0.8682171
TAC	3		0.0058140	0.0156250	0.3720930
TAG	4		0.0077519	0.0156250	0.4961240
TAT	1		0.0019380	0.0156250	0.1240310
TCA	10		0.0193798	0.0156250	1.2403101
TCC	6		0.0116279	0.0156250	0.7441860
TCG	7		0.0135659	0.0156250	0.8682171
TCT	10		0.0193798	0.0156250	1.2403101
TGA	4		0.0077519	0.0156250	0.4961240
TGC	9		0.0174419	0.0156250	1.1162791
TGG	14		0.0271318	0.0156250	1.7364341
TGT	5		0.0096899	0.0156250	0.6201550
TTA	2		0.0038760	0.0156250	0.2480620
TTC	10		0.0193798	0.0156250	1.2403101
TTG	7		0.0135659	0.0156250	0.8682171
TTT	7		0.0135659	0.0156250	0.8682171

Other	0		0.0000000	0.0000000	10000000000.0000000

Output file format

The output format consists of:

Header information and comments are preceeded by a '#' character at the start of the line.

The Word size and the Total count are then given on separate lines,

The headers of the columns of results are preceeded by a '#'

The results columns are: the sub-sequence word, the observed frequency, the expected frequency (which will be read from the input file if one is given, else it is a simple inverse of the number of words of the size specified that can be constructed), the ratio of the observed to expected frequency.

After a blank line at the end, the results of 'Other' words is given - this is the number of words with a sequence which has IUPAC ambiguity codes or other unusual characters in.

Output files for usage example

File: result3.comp

#
# Output from 'compseq'
#
# The Expected frequencies are calculated on the (false) assumption that every
# word has equal frequency.
#
# The input sequences are:
#	X65923


Word size	2
Total count	517

#
# Word	Obs Count	Obs Frequency	Exp Frequency	Obs/Exp Frequency
#
AA	45		0.0870406	0.0625000	1.3926499
AC	20		0.0386847	0.0625000	0.6189555
AG	45		0.0870406	0.0625000	1.3926499
AT	14		0.0270793	0.0625000	0.4332689
CA	34		0.0657640	0.0625000	1.0522244
CC	43		0.0831721	0.0625000	1.3307544
CG	25		0.0483559	0.0625000	0.7736944
CT	37		0.0715667	0.0625000	1.1450677
GA	31		0.0599613	0.0625000	0.9593810
GC	43		0.0831721	0.0625000	1.3307544
GG	46		0.0889749	0.0625000	1.4235977
GT	28		0.0541586	0.0625000	0.8665377
TA	15		0.0290135	0.0625000	0.4642166
TC	33		0.0638298	0.0625000	1.0212766
TG	32		0.0618956	0.0625000	0.9903288
TT	26		0.0502901	0.0625000	0.8046422

Other	0		0.0000000	0.0000000	10000000000.0000000

Output files for usage example 2

File: result6.comp

#
# Output from 'compseq'
#
# Words with a frequency of zero are not reported.
# The Expected frequencies are calculated on the (false) assumption that every
# word has equal frequency.
#
# The input sequences are:
#	X65923


Word size	6
Total count	513

#
# Word	Obs Count	Obs Frequency	Exp Frequency	Obs/Exp Frequency
#
AAAAAA	6		0.0116959	0.0002441	47.9064327
AAAAAG	1		0.0019493	0.0002441	7.9844055
AAAAGC	1		0.0019493	0.0002441	7.9844055
AAAAGT	1		0.0019493	0.0002441	7.9844055
AAACAG	1		0.0019493	0.0002441	7.9844055
AAACGG	1		0.0019493	0.0002441	7.9844055
AAAGCC	1		0.0019493	0.0002441	7.9844055
AAAGTG	1		0.0019493	0.0002441	7.9844055
AAAGTT	1		0.0019493	0.0002441	7.9844055
AACAGG	1		0.0019493	0.0002441	7.9844055
AACCGG	1		0.0019493	0.0002441	7.9844055
AACGGT	1		0.0019493	0.0002441	7.9844055
AACGTT	1		0.0019493	0.0002441	7.9844055
AACTCT	1		0.0019493	0.0002441	7.9844055
AAGAAG	6		0.0116959	0.0002441	47.9064327
AAGACA	1		0.0019493	0.0002441	7.9844055
AAGATC	1		0.0019493	0.0002441	7.9844055
AAGCCA	1		0.0019493	0.0002441	7.9844055
AAGCGG	1		0.0019493	0.0002441	7.9844055
AAGGCT	1		0.0019493	0.0002441	7.9844055
AAGGGC	1		0.0019493	0.0002441	7.9844055
AAGGTG	1		0.0019493	0.0002441	7.9844055
AAGTAG	1		0.0019493	0.0002441	7.9844055
AAGTCG	1		0.0019493	0.0002441	7.9844055
AAGTCT	1		0.0019493	0.0002441	7.9844055
AAGTGA	1		0.0019493	0.0002441	7.9844055
AAGTTC	1		0.0019493	0.0002441	7.9844055
AATAAA	1		0.0019493	0.0002441	7.9844055
AATATG	1		0.0019493	0.0002441	7.9844055
AATGCC	1		0.0019493	0.0002441	7.9844055
AATTCT	1		0.0019493	0.0002441	7.9844055
ACAACC	1		0.0019493	0.0002441	7.9844055
ACACAC	1		0.0019493	0.0002441	7.9844055


  [Part of this file has been deleted for brevity]

TGAGGC	1		0.0019493	0.0002441	7.9844055
TGCAGC	1		0.0019493	0.0002441	7.9844055
TGCAGT	1		0.0019493	0.0002441	7.9844055
TGCCAA	1		0.0019493	0.0002441	7.9844055
TGCCCA	1		0.0019493	0.0002441	7.9844055
TGCCCC	1		0.0019493	0.0002441	7.9844055
TGCGGG	1		0.0019493	0.0002441	7.9844055
TGCTCC	1		0.0019493	0.0002441	7.9844055
TGCTGG	1		0.0019493	0.0002441	7.9844055
TGCTTG	1		0.0019493	0.0002441	7.9844055
TGGAAA	1		0.0019493	0.0002441	7.9844055
TGGAAG	1		0.0019493	0.0002441	7.9844055
TGGAGG	4		0.0077973	0.0002441	31.9376218
TGGCAA	1		0.0019493	0.0002441	7.9844055
TGGCAG	1		0.0019493	0.0002441	7.9844055
TGGCCA	1		0.0019493	0.0002441	7.9844055
TGGCCC	1		0.0019493	0.0002441	7.9844055
TGGCTT	1		0.0019493	0.0002441	7.9844055
TGGGAC	1		0.0019493	0.0002441	7.9844055
TGGGCC	1		0.0019493	0.0002441	7.9844055
TGGTTC	1		0.0019493	0.0002441	7.9844055
TGTAAT	1		0.0019493	0.0002441	7.9844055
TGTAGC	1		0.0019493	0.0002441	7.9844055
TGTCAA	1		0.0019493	0.0002441	7.9844055
TGTCCG	1		0.0019493	0.0002441	7.9844055
TGTGCC	1		0.0019493	0.0002441	7.9844055
TTAAGT	1		0.0019493	0.0002441	7.9844055
TTAGTT	1		0.0019493	0.0002441	7.9844055
TTCAGT	2		0.0038986	0.0002441	15.9688109
TTCATG	1		0.0019493	0.0002441	7.9844055
TTCCCT	1		0.0019493	0.0002441	7.9844055
TTCCTC	1		0.0019493	0.0002441	7.9844055
TTCGAG	1		0.0019493	0.0002441	7.9844055
TTCGCG	1		0.0019493	0.0002441	7.9844055
TTCTCG	1		0.0019493	0.0002441	7.9844055
TTCTCT	1		0.0019493	0.0002441	7.9844055
TTCTGG	1		0.0019493	0.0002441	7.9844055
TTGCCC	1		0.0019493	0.0002441	7.9844055
TTGGAG	1		0.0019493	0.0002441	7.9844055
TTGGCA	1		0.0019493	0.0002441	7.9844055
TTGTAA	1		0.0019493	0.0002441	7.9844055
TTGTCA	1		0.0019493	0.0002441	7.9844055
TTGTCC	1		0.0019493	0.0002441	7.9844055
TTGTGC	1		0.0019493	0.0002441	7.9844055
TTTCTC	2		0.0038986	0.0002441	15.9688109
TTTGGC	1		0.0019493	0.0002441	7.9844055
TTTGTA	1		0.0019493	0.0002441	7.9844055
TTTGTC	2		0.0038986	0.0002441	15.9688109
TTTTGT	1		0.0019493	0.0002441	7.9844055

Other	0		0.0000000	0.0000000	10000000000.0000000

Output files for usage example 3

File: result3.comp

#
# Output from 'compseq'
#
# Only words in frame 2 will be counted.
# The Expected frequencies are taken from the file: ../../data/prev.comp
#
# The input sequences are:
#	X65923


Word size	3
Total count	172

#
# Word	Obs Count	Obs Frequency	Exp Frequency	Obs/Exp Frequency
#
AAA	7		0.0406977	0.0329457	1.2352955
AAC	3		0.0174419	0.0096899	1.8000042
AAG	11		0.0639535	0.0348837	1.8333344
AAT	3		0.0174419	0.0077519	2.2500110
ACA	1		0.0058140	0.0096899	0.6000014
ACC	4		0.0232558	0.0116279	2.0000012
ACG	1		0.0058140	0.0038760	1.4999880
ACT	3		0.0174419	0.0135659	1.2857135
AGA	1		0.0058140	0.0232558	0.2500002
AGC	2		0.0116279	0.0135659	0.8571423
AGG	0		0.0000000	0.0310078	0.0000000
AGT	0		0.0000000	0.0193798	0.0000000
ATA	0		0.0000000	0.0038760	0.0000000
ATC	1		0.0058140	0.0058140	0.9999920
ATG	3		0.0174419	0.0135659	1.2857135
ATT	1		0.0058140	0.0038760	1.4999880
CAA	1		0.0058140	0.0193798	0.3000007
CAC	2		0.0116279	0.0116279	1.0000006
CAG	9		0.0523256	0.0251938	2.0769229
CAT	3		0.0174419	0.0096899	1.8000042
CCA	0		0.0000000	0.0232558	0.0000000
CCC	3		0.0174419	0.0251938	0.6923076
CCG	1		0.0058140	0.0155039	0.3749994
CCT	2		0.0116279	0.0193798	0.6000014
CGA	1		0.0058140	0.0038760	1.4999880
CGC	5		0.0290698	0.0193798	1.5000035
CGG	4		0.0232558	0.0174419	1.3333303
CGT	2		0.0116279	0.0077519	1.5000074
CTA	1		0.0058140	0.0096899	0.6000014
CTC	4		0.0232558	0.0213178	1.0909106
CTG	7		0.0406977	0.0193798	2.1000049
CTT	3		0.0174419	0.0213178	0.8181829
GAA	3		0.0174419	0.0213178	0.8181829
GAC	1		0.0058140	0.0116279	0.5000003
GAG	7		0.0406977	0.0193798	2.1000049
GAT	2		0.0116279	0.0077519	1.5000074
GCA	2		0.0116279	0.0135659	0.8571423
GCC	10		0.0581395	0.0348837	1.6666677
GCG	1		0.0058140	0.0155039	0.3749994
GCT	3		0.0174419	0.0193798	0.9000021
GGA	2		0.0116279	0.0251938	0.4615384
GGC	8		0.0465116	0.0329457	1.4117663
GGG	1		0.0058140	0.0135659	0.4285712
GGT	5		0.0290698	0.0174419	1.6666629
GTA	2		0.0116279	0.0116279	1.0000006
GTC	6		0.0348837	0.0174419	1.9999955
GTG	6		0.0348837	0.0155039	2.2499965
GTT	3		0.0174419	0.0096899	1.8000042
TAA	3		0.0174419	0.0135659	1.2857135
TAC	1		0.0058140	0.0058140	0.9999920
TAG	0		0.0000000	0.0077519	0.0000000
TAT	0		0.0000000	0.0019380	0.0000000
TCA	3		0.0174419	0.0193798	0.9000021
TCC	1		0.0058140	0.0116279	0.5000003
TCG	0		0.0000000	0.0135659	0.0000000
TCT	3		0.0174419	0.0193798	0.9000021
TGA	0		0.0000000	0.0077519	0.0000000
TGC	1		0.0058140	0.0174419	0.3333326
TGG	1		0.0058140	0.0271318	0.2142856
TGT	1		0.0058140	0.0096899	0.6000014
TTA	1		0.0058140	0.0038760	1.4999880
TTC	1		0.0058140	0.0193798	0.3000007
TTG	0		0.0000000	0.0135659	0.0000000
TTT	5		0.0290698	0.0135659	2.1428558

Other	0		0.0000000	0.0000000	10000000000.0000000

Data files

None.

Notes

The maximum word size is limited to 4 for proteins, and 6 for nucleotide sequences.

Large word sizes are not appropriate for the compseq algorithm. All possible words will be stored and reported. The algorithm is designed to generate useful information for word sizes expected to occur at least once in the input sequence.

The results are held in an array in memory before being written to a file. For large values of wordsize (over about 7 for nucleic, 5 for protein), you may run out of memory or generate a very large output file.

There is no way for compseq to guess what the true expected frequency should be for each word. It can however read in the result of a previous compseq analysis and use this to set the expected frequencies of the subsequences. In this case, the input sequences under investigation should be representative of those used for the previous compseq analysis. It is down to your biological expertise to ensure the sequences are genuinely "representative", for instance, you might select a group of sequences belonging to the same taxonomic rank such as genus or species.

The file of expected frequencies is specified by name with the -infile qualifier. The word size in the current run must be the same as the one in this results file. Obviously, you should use a file produced from protein sequences if you are counting protein sequence word frequencies, and you must use one made from nucleotide frequencies if you are analysing a nucleotide sequence.

As an alternative to using -infile, the expected frequencies of words may be calculated from the observed frequency of single bases or residues in the sequences. To do this, specify the -calcfreq qualifier. If you are reporting a word size of 1 (single bases or residues) then there is no point in using this option because the calculated expected frequency will be equal to the observed frequency.

Calculating the expected frequencies like this will give an approximation of the expected frequencies that you might get by using an input file of frequencies produced by a previous run of this program. If an input file of expected word frequencies has been specified then the values from that file will be used instead of this calculation of expected frequency from the sequence, even if 'calcfreq' is set to be true.

References

None.

Warnings

Diagnostic Error Messages

"The word size is too large for the data structure available."
You chose a word size that cannot be stored by the program.
"Insufficient memory - aborting."
You do not have enough memory - use a machine with more memory.
"The word size you are counting (n) is different to the word size in the file of expected frequencies (n)."
You chose different word sizes in the run of compseq that produced your results file used to display the expected word frequencies to the word size used in this run of compseq.
"The 'Word size' line was not found, instead found:"
You appear to be trying to read a corrupted compseq results file

Exit status

It always exits with status 0 unless one of the above error conditions is found

Known bugs

This program can use a large amount of memory is you were allowed to specify a large word size (7 or above). This may impact the behaviour of other programs on your machine.

If you run out of memory, you may see the program crash with a generic error message that will be specific to your machine's operating system, but will probably be a warning about writing to memory that the program does not own (eg "Segmentation fault" on a Solaris machine)

This is not a bug, it is a feature of the way this program grabs large amounts of memory. The maximum word size is restricted to avoid this problem.

See also

Program name Description
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq Back-translate a protein sequence to a nucleotide sequence
banana Plot bending and curvature data for B-DNA
btwisted Calculate the twisting in a B-DNA sequence
chaos Draw a chaos game representation plot for a nucleotide sequence
dan Calculate nucleic acid melting temperature
density Draw a nucleic acid density plot
emowse Search protein sequences by digest fragment molecular weight
freak Generate residue/base frequency table or plot
isochore Plot isochores in DNA sequences
mwcontam Find weights common to multiple molecular weights files
mwfilter Filter noisy data from molecular weights file
oddcomp Identify proteins with specified sequence word composition
pepdigest Report on protein proteolytic enzyme or reagent cleavage sites
pepinfo Plot amino acid properties of a protein sequence in parallel
pepstats Calculate statistics of protein properties
wordcount Count and extract unique words in molecular sequence(s)

Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Completed 2 March 2000
5 April 2001 (version 1.12.0) - the operation of the option '-reverse' has changed. It is now 'False' by default instead of being 'True' by default for nucleic sequences. Too many people were getting confused by the counts being done on both senses, so this is now done on only the forward sense by default.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None