Within EMBOSS you will find around hundreds of program (applications) covering areas such as:
- Sequence alignment,
- Rapid database searching with sequence patterns,
- Protein motif identification, including domain analysis,
- Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats,
- Codon usage analysis for small genomes,
- Rapid identification of sequence patterns in large scale sequence sets,
- Presentation tools for publication,
and much more.
Popular applications include:
Link to local EMBOSS documentation.
prophet Gapped alignment for profiles. infoseq Displays some simple information about sequences. water Smith-Waterman local alignment. pepstats Protein statistics. showfeat Show features of a sequence. palindrome Looks for inverted repeats in a nucleotide sequence. eprimer3 Picks PCR primers and hybridization oligos. profit Scan a sequence or database with a matrix or profile. extractseq Extract regions from a sequence. marscan Finds MAR/SAR sites in nucleic sequences. tfscan Scans DNA sequences for transcription factors. patmatmotifs Compares a protein sequence to the PROSITE motif database. showdb Displays information on the currently available databases. wossname Finds programs by keywords in their one-line documentation. abiview Reads ABI file and display the trace. tranalign Align nucleic coding regions given the aligned proteins.
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