Hi Galih, Thank you for your feedback on the genome browser. We will keep your suggestion in mind for future revisions of our sequence retrieval tools however it is unlikely that we will be conducting such revisions in the near future.
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu GALIH Kunarso wrote: > Hi UCSC, > > > > I have a suggestion regarding the Table Browser. Currently whenever we > want to extract either sequences or BED coordinates from the Table > Browser we have the option to add bases Upstream and Downstream of the > features that we're interested in, but this is from the Boundaries of > the feature. > > May I suggest that you add another functionality of extracting the extra > bases from the Centre of the features itself so that in the end I can > easily get for example 100 bp-long regions centered on Exapted Repeats. > > > > I do a lot of binding site analysis and often I need to extract 200 > bp-long sequences centered on the binding regions identified by > ChIP-chip for motif analysis. At the moment I have to format the BED > files on my own to get those 200 bp-long regions before submitting them > as Custom Track and extracting the sequences. I figure if you have that > functionality built-in into Table Browser users can just input their > original BED file and extract whatever length of sequences centered on > those regions easily instead of creating a new BED format for every > length of intervals they require. > > > > Thank you for your attention. > > > > Regards, > > > > Galih Kunarso > > Computational and Mathematical Biology > > Genome Institute of Singapore > > 60 Biopolis Street, Genome #02-01, Singapore 138672 > > DID: 6478-8661 Fax: 6478-9058 > > > > -------------------------------------------------------- > > This e-mail is confidential and may be privileged. If you > > are not the intended recipient, please delete it and notify > > us immediately. Please do not copy or use it for any purpose, > > or disclose its contents to any other person. Thank you. > > -------------------------------------------------------- > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
