Increase the input sequences in pfamScan

Question

[K.Gee]

Hello everybody.

I'm trying to use PfamScan via the command line for a file containing 600 protein sequences. I typed the command line below:

pfarmScan.pl --email [e-mail] --database pfam-a --sequence file.fa --evalue 1e-5 --format txt

I got this error:

http status: 400 Bad Request  Invalid parameters: 
Input Sequence -> Only 100 sequence allowed at /home/kgee/bin/pfarmScan.pl line 279.

I also tried to use the online version, but I got the same error. I am wondering if there is any way to increase the number of the input sequences?

Thank you in advance

[5heikki]

Install it locally?

[K.Gee]

no. I just I downloaded the perl script from here

Answer 1

[h.mon]

When using a web server to perform analysis, it is good manners (and good practice) to not hammer the server with lots of jobs. Most servers will enforce some kind of limit - as in this case, the limit of 100 sequences per submission. The EBI web server (I guess you are using pfam_scan.pl?) has the following request:

Important Note

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.

What tool are you using? The command line you posted says pfarmScan.pl, for which I found no mention at all in search engines. There is a pfam_scan.pl from EBI, but the command-line options doesn't seem to match the tool you are using. Automating the submission of jobs (in a way that respects the server limits) could be achieved in several ways (e.g, with GNU Parallel), but, without knowing which tool you are using, it is impossible to suggest more concrete solutions.

[K.Gee]

ok I see... I downloaded the perl script from here, (Perl option in REST API). I was thinking of avoid scripting and running the pfam 6 times... But I got your point. Thanks for replying me.