samt99_filter.pl

Written by Osvaldo Graña, Protein Design Group (CNB-CSIC), December 2000

This application changes the format of SAMT99 files to a new format readable by THREADLIZE

("http://www.cnb.uam.es/~pazos/threadlize" Pazos, Rost & Valencia (1999) Bioinformatics 15(12):1062-1063)

It can also include the SAMT99 secondary structure prediction in the output.

1.- HOW TO USE IT WITHOUT SECONDARY STRUCTURE PREDICTION (TWO ARGUMENTS)

email, then you must check the following options: "Pretty Align", "A2M", and "email results".

When you've got your email answers from SAMT99 you save the "*dbhits.txt" and "*pairwise.pa" files, those are the arguments for

samt99_filter.pl

For example, if you have saved from SAMT99 the files "namedbhits.txt" and "namepairwise.pa", you type the following in your

Unix/Linux terminal:

samt99_filter.pl namedbhits.txt namepairwise.pa > results

in this case your results will be in the file "results", you can use another file name for your results.

By doing it this way, you will find in your results file the list of hits

and the corresponding alignments.

2.- HOW TO USE IT INCLUDING SECONDARY STRUCTURE PREDICTION (THREE ARGUMENTS)

You do the same as before, but you also put your query sequence in "http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html",

your email, and just check the option "return secondary structure prediction in format(s): CASP" and the option "email results".

Once you've got your email answers from SAMT99 you save the "*casp.ss" file, it is the third argument for samt99_filter.pl

Taking the last example: "namedbhits.txt", "namepairwise.pa" and "namecasp.ss" you type the following in your Unix/Linux terminal:

samt99_filter.pl namedbhits.txt namepairwise.pa namecasp.ss > results

with your results in the file "results".

By doing it this way, you will find in your results file the list of hits, the corresponding alignments and the predicted secondary structure.

IN BOTH CASES, the file "results" can be used as input by THREADLIZE:

threadlize results &

LICENSE TERMS:

This program is free licensed for academic and non-profit users. Private users, please, contact Osvaldo Graña (osvaldog@cnb.uam.es).

Please, do not modify the code.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.

Osvaldo Graña

Protein Design Group (CNB-CSIC)

Campus Universidad Autonoma.

Cantoblanco. 28049 Madrid.

Tlf: +34-91-5854570. Fax: +34-91-5854506.