How can I download the alignments of EST sequences to genomic sequences?
You can extract it from the GFF files that we provide with every release of WormBase. For more information on GFF files see: http://www.sanger.ac.uk/Software/formats/GFF/ Basically, we release one GFF file per chromosome and this contains the coordinates and details of most features that we can map onto chromosome base pair coordinates. These files are accesible from the main WormBase page (see the Feature table links on the right) and should also be on the WormBase and Sanger Institute FTP sites. You will need to extract only a subset of these files, i.e. lines that match the pattern ‘BLAT_EST_’. This is very easy to do if you have access to a UNIX/Linux system (use the ‘grep’ command). E.g.
Related Questions
- Interval and BED format Extract Genomic DNA tool under Fetch sequences section returns one less nucleotide for each of my intervals. Is this a bug?
- My study has identified novel insertion sequences and I don have a genomic coordinate for these. How can I submit these to dbVar?
- How can I download the alignments of EST sequences to genomic sequences?
