How To Generate Pssm Files From Protein Sequences

Question

[Yu Hsiung]

I have some protein sequence and its id.

How can I use them to generate pssm files?

• 1: From web site by perl
• 2: or by one program in my local pc

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for example, I use one seq. from one of RS126 that filename is "1acx.concsie" the id is "lacx" the seq. is

APAFSVSPASGASDGQSVSVSVAAAGETYYIAQCAPVGGQDACNPATATSFTTDASGAASFSFTVRKSYAGQTPSGTPVGSVDCATDACNLGAGNSGLNLGHVALTFG

How can I use them to generate pssm files?

• 1. Parsing web site by perl
• 1. Get one program that can generate pssm file in local pc in Linux system

Answer 1

[Anima Mundi]

Hi, you should use the IDs to recall, from the RefSeq database, quality full length sequences. You should list their FASTAs in a single file, then you could provide them to Glam2, both via remote scripting or, better, in local. From the Glam2 output you can choose the best matrix and put it into a separate file. The PSSMs obtained would be in MEME format, you can format them in the desired format in a second moment (as the MEME format is highly informative).