[Bioperl-l] query

[zhabiz golkar]

Dear Sir/Madam
We have done the sequencing of about 50 HIV +ve samples. We have used HIV BLAST database. And identified the subtypes,.. we have used 2 pair primers( reverse and forward) means we have 4 seq. for each sample. NOW
1-      We are looking for gag, reverse transcriptase and protease(POL) regions of each sample and 
2-      We want to do comparison of these regions which each other. Please note , when we use database, they do the comparison with the reference genome (HIV-1). But we need to compare theses regions among the isolates. And clustalW and X also is not highlighting the specific region .
I would be great full if you can give suggestion or send the link or software name that we can do application .
 
Looking forward to hear you . and thanking you in anticipation 
Regards
Dr.Zhabiz