Entering edit mode
10.5 years ago
eddie.im
▴
140
Hello,
Is there any software to map sequences against a genome and get genomic coordates/genomic ranges? I used several tools to get short sequences of ncRNA, but in the process i lost track of the genomic location of these, i have tried blast but it doens't perform very well, even when set to ungapped and 100% identity, i think that is because the sequences are too short, their pieces align to more than on spot on genome. I have used task ='blastn-shot' but it doens't worked either.
I have used Artemis and locate the regions by pattern search, but it's very unpratical since i have few hundreds of sequences. So what i'm looking for is some command line software or graphical that can do this in an automated way.
Thanks,
I don't see how BLAT results would be different from BLAST, the same problem should arise from BLAT that is pieces of the sequences aligning everywhere. I will give it a shot however. Thanks.
Did the pieces originally come from the same region? If so, but the individual pieces are so short that they align in multiple places, could you use BLAT (or indeed, BLAST) to find all those alignments, and then find the locations where there are clusters of pieces aligning in the same area, and do a sort of assembly. You can join your pieces that are within some distance of each other, and then look for the longest such 'contigs'