Formatting BLAT or BLAST results

BLAT at UCSC

Use for example this fasta file (several exons from GUSB) . BLAT it on the human genome (since these are exons from a human gene).
Be carefull ! Exons downloaded from ENSEMBL have gene ID (here ENST00000304895) as first word and this while return an error (duplicated ids).

As shown above, the raw result is not very easy to analyze quickly.
Simply save the resulting html file as for example SCL_exons_hgBlat.htm.

BLAT at Ensembl.

Set the SearchTool to BLAT.
Use for example this fasta file (several exons from GUSB) . BLAT it on the human genome (since these are exons from a human gene). Now on this server this can be a bit complicated, because each exon is treated separately, as shown below:

Now you need to successively hit each "RawResult", and save each page under a different name.

Stand alone BLAT.

Download the program from UCSC, install your database on a local port. Run it as detailled. Use the output file as you would from UCSC web server, except this will be a text file and not an html file.

BLAST at Ensembl.

The procedure is exactly identical (but the response is much longer to obtain !).

Stand alone BLAST

Download the program from the NCBI ftp site. Format your database and run your blastn. Then the procedure is identical to that used for EBI, except that all results will be in a single file.
Make sure you use the "-m 7" option, that create a XML ouput file. Save it with an extension like ".txt", ".out" or ".BLAST".