EMBOSS
From Vd
General Information
EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
Within EMBOSS you will find around hundreds of programs (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:
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.
Home Page
http://emboss.sourceforge.net/