Hi List, We now have the Rebase locally installed. Strangely, I see a new error;
"Input nucleotide sequence(s): chr10.fa Uncaught exception: Allocation failed, insufficient memory available, raised at ajstr.c:2170" Above example is just for testing with chromosome 10, I plan to do either whole genome (all 23 chromosomes) or do 23 times with each chromosome. I have tested running on a queue with higher memory using following command; qsub -q normal-ib /path/restrict -sequence chr10.fa -enzymes hinfI -fragments -outfile chr10.res Then it threw following error; "Unable to run job: Script length does not match declared length." It may not be the restrict problem, I was just throwing it in here to see if anyone else have had seen such a problem. Any guess. Thanks, perdeep From: [email protected] [mailto:[email protected]] Sent: Tuesday, February 23, 2010 12:56 AM To: Mehta, Perdeep Cc: emboss; [email protected] Subject: Antwort: [EMBOSS] restrict Hi, [email protected] schrieb am 23/02/2010 00:21:38: > I have a few questions on EMBOSS restriction analysis and will > appreciate any ideas or thoughts on these. > > 1. What Rebase file we need to download to get "restrict" working? I > tried but there are files with different formats. Go to the /pub/rebase dir on ftp.neb.com. Download the withrefm.xxx and proto.xxx files (xxx stands for the version number, just take the latest that's there) Run rebaseextract -infile withrefm.xxx -protofile proto.xxx This reformats the neb files for use with emboss. You should now see 4 files embossre.... in the REBASE directory > 2. Is there a maximum size limit of a nucleotide sequence that I can > use? Can I use the whole Human genome or at least a full chromosome > to digest with a particular restriction enzyme? I'm not sure about the whole genome but I have used it for individual chromosomes without problems. > 3. What program can give me the list of all possible fragments > generated as well? Since I have not seen the output of "restrict", > perhaps that is already doing that. You can run restrict with the option -fragments to get them. Hope this helps, David. ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
