BLAST search - (Feb/28/2005 )

In my experiment, genomic dna was digested into small fragments with different size and then these fragments were cloned and sequenced. AFter sequencing, I tried to do the NCBI BLAST search to find the idenities of these fragments. However, I could only find the fragment was from chromosome 5 WGS supercontig or something like that. Have you guys done something like this? Which softwares do you use? ensembl BLAST, NCBI BLAST search or something else?

I like to use the Golden Path at UCSC. Here's the link: genome.ucsc.edu
There you have a BLAT option, where you can introduce your sequence, and a Browser, where you can look for your genes by the name.
The main feature of this site for me are its graphics, much more user-friendly than the NCBI or ENSEMBL. Just past your sequence and you will get a map of the relevant chromosome, with your sequence aligned to it, and all the known genes and ESTs that map to this zone.
Hope that helps!

I use NCBIs BLASTx mostly. If you are not getting much of an idea of the gene's identity you can translate that sequence to the amino acid sequence using ExPASy- find the open reading frame or the one with the least amount of stop codons and use that as your translation sequence. Put that sequence into NCBIs conserved domain database and see what kind of domains it may contain, this will give you some idea of function. If nothing else, compare your results from BLASTx to BLASTp results and see if they overlap.

Conserved Domian Database
ExPASy translate