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Old 02-27-2009, 01:56 PM   #1
found
Junior Member
 
Location: Miami

Join Date: Feb 2009
Posts: 8
Question So many software for alignment!!!

Hi,

I am new to the area of mRNA-Seq data analysis, actually also not "old" to the bioinformatics.
Recently, I have read a paper involved in the mapping of mRNA-Seq data to the human genome by ELAND. I am very interested in the mapping result and want to do some data mining for my own purpose. And the author only gives out the original mRNA-Seq data.
I have browsed this forum for days and learned a lot. first thing is that ELAND is not available for me. I found that someone have listed so many software for short read sequence alignment and I feel really confused about that which one is suitable for me. That's why I am here to get some suggestions from experienced expert.

My object is to map all of these mRNA-Seq to a database which includes the human genome and my own set of sequences(56bp). At most two mismatches and no gaps are allowed. Since a small part of sequences my contain symbol '.' such as "ATCTAT.CGTACG.GCTAGTGGTGAAGG", the software should not filter '.' out and consider it as a mismatch during alignment.

Can you recommend a software to implement this purpose. Of course, both accuracy and speed are important. I think accuracy is more important if they can not be satisfied simultaneously.

Last edited by found; 02-27-2009 at 02:03 PM.
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