FASTA sequences

PAMPA processes amino-acid sequences. For that, it uses the standard FASTA format with UniprotKB-like header.

For each sequence, the first line starts with a greater-than character (>) followed by some sequence identifier (SeqID), which is provided for informational purposes and can be customized by the user. Additionally, this line must contain three mandatory fields:

OS : scientific name of the organism

OX : taxonomic identifier of the organism

GN : gene name

Other fields are ignored, which means that Uniprot sequences are recognized. The other lines of the file are the sequence representation, with one letter per amino acid.

>P02453 OS=Bos taurus OX=9913 GN=COL1A1 
MFSFVDLRLLLLLAATALLTHGQEEGQEEGQEEDIPPVTCVQNGLRYHDRDVWKPVPCQI
CVCDNGNVLCDDVICDELKDCPNAKVPTDECCPVCPEGQESPTDQETTGVEGPKGDTGPR
GPRGPAGPPGRDGIPGQPGLPGPPGPPGPPGPPGLGGNFAPQLSYGYDEKSTGISVPGPM
GPSGPRGLPGPPGAPGPQGFQGPPGEPGEPGASGPMGPRGPPGPPGKNGDDGEAGKPGRP
GERGPPGPQGARGLPGTAGLPGMKGHRGFSGLDGAKGDAGPAGPKGEPGSPGENGAPGQM

Each file can contain as many sequences as needed. PAMPA can also process multiple FASTA files from a specified directory.

Note on the taxonomic identifier OX

The main purpose of the taxonomic identifier is to create a link between the taxon and the taxonomy. So, if you use the NCBI taxonomy, you should also use NCBI TaxID in the FASTA heading. These TaxIDs can be found here : https://www.ncbi.nlm.nih.gov/taxonomy. Sequences downloaded from Uniprot come with the NCBI TaxID.

If the sequences does not have any standard TaxID, you can define your own TaxID.