FASTA sequences

PAMPA processes amino-acid sequences. For that, it uses the standard FASTA format with UniprotKB-like header. 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, such as assigned by the NCBI (for example). This identifier should be the same as the one used in the taxonomy file.

GN : gene name

The other lines are the sequence representation, with one letter per amino acid.

For example:

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