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,