1) blast and find the pos index of ur target

2) use any method (script or manual) to find the upstream and downstream seqs

What Atongsa says is basically how it's done. I suppose to expand a little bit:

• the Bio* toolkits (e.g. biopython) can parse BLAST results so that you get the accession against which you had a hit, and where that was in the sequence.
• with the accession number of the hit you go and fetch the full sequence and splice out the parts upstream and downstream.
• I don't see how this could be done without some basic programming but if you know basically any common scripting language (R, python, ruby, perl...) this is pretty straightforward.

Hello Rutger and Atongsa,

Thank you for your responses. I guess I should clarify, I know how to do this manually one by one through NCBI. The problem is the time, doing this manually for 400+ sequences against 26 genomes is a bit much. Thus, I was wondering if people had suggestions for automating this, i.e. does anyone have a suggestion as to how to automate a blast search for 400+ sequences at once across all Glires reference representative genomes in NCBI and then pull alignments of the top hits for each sequence into an fasta alignment?

I am familiar with R, python, and perl and do cluster computing and have tried a few methods but keep having problems with doing this all at once through NCBI with out having to download and create a database of all genomes locally. Any suggestions would be appreciated.

Best Regards