Dear Wadim, The current 0.7 version of BioMart does not support retrieving sequences from chromosomal regions that are independent from annotations. The new 0.8 pre-release version does not have this option either as it supports the same options as 0.7. I think your suggestion is very good and it should not be difficult to write a plugin to extract sequence from chromosomal regions regardless if they contain genes or not. i am forwarding your email to [email protected] this can be added to the list of requested features for 0.8
a On Fri, Jul 15, 2011 at 2:53 PM, wadim kapulkin <[email protected]>wrote: > Dear Arek, > > Below I forwarded the e-mail I wrote to ensembl helpdesk. It concerns of > the aspect of biomart I think it would be very useful for end users like > myself. In brief searching across the options for mining of the DNA > associated information (i.e.coding vs noncoding etc) i think it would help > if one could just choose 'multiple subrange fasta sequences from any given > chromosome/dataset ' regardless of theirs annotation. > > Help and/or comments would be gladly appreciated. > > Kind regards > Wadim > > ----- Forwarded Message ---- > *From:* Ensembl Helpdesk via RT <[email protected]> > *To:* [email protected] > *Sent:* Fri, 15 July, 2011 14:06:13 > *Subject:* [Ensembl #224136] AutoReply: ? extracting multiple subrange > fasta sequences from given chromosome / dataset - www.ensembl.org > > Greetings, > > A ticket has been created regarding: > "? extracting multiple subrange fasta sequences from given chromosome / > dataset - www.ensembl.org", > a summary of which appears below. > > Your ticket has been assigned an ID of [Hinxton #224136]. > > We will look into your problem as soon as possible. > > In order to add more information to this ticket please include the string: > > [Hinxton #224136] > > in the subject line of all future correspondence. To do so, > you may reply to this message. > > Best regards, > Ensembl Helpdesk > [email protected] > > ------------------------------------------------------------------------- > Support question from www.ensembl.org > > Date: 2011-07-15 19:06:02 > Name: Wadim Kapulkin > Referer: http://www.ensembl.org > Last Search: -none- > User agent: Mozilla/5.0 (Macintosh; U; PPC Mac OS X 10_4_11; en) > AppleWebKit/533.19.4 (KHTML, like Gecko) Version/4.1.3 Safari/533.19.4 > > Comments: > > Dear All > > Please excuse me if i am asking trivia. > > I would be quite keen o knowing as how to extract multiple subrange fasta > sequences from any given chromosome / dataset ? > > I have been trying to extract with biomart/martview > [www.ensembl.org/biomart/martview/6083fbcbedaa0a1da13cf3e106be545b] > specifying the dataset Canfam_2.0 and setting the filters for chromosome (X > in example below) and than for (X:42152150:42169554:1,X:2152150:2169554:1) > via 'Multiple Chromosomal Regions' window . > > It doesn't seem to export the same sequence as idividual exports ... > > > Help/comments would be gladly appreciated > > [Perhaps I could receive example file - do be upload- in suitable format > forcing the multiple download? - i just guess i am not specifying the > download wright] > > kind regards > wadim kapulkin > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. >
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