I have a 454 sequencing of streptococcus pneumoniae resistant to trimethoprim-sulfamethoxazole antibiotic (SRP000185). I am a newbie so I don't know how to initiate? My aim is to find mutation and SNP which are responsible for it. I am working on a linux platform. I have downloaded a sequence but don't know what should do? Could any one help me please?
Go through this paper, might be helpful
http://www.biomedcentral.com/1471-2164/13/S7/S23
You can simply perform sequence alignments and check mutation comparatively.
If it was me I'd check your drug-target genes first, ie DHFR and DHPS respectively (http://www.ncbi.nlm.nih.gov/pubmed/18500934). Is the clone resistant to other PDR pump substrates? If so, check these sequences or the TF's controlling them. If no sequence divergence from wild type is shown here then you will have to do whole genome alignments with an isogenic wild type sequence.
Thanks James Matthews and Anuj Ranjan for your valuable answers. I am starting with genome resistent sequence and its sra format so I converted in the SFF formats. what should do next?
Comparing the whole genome shotgun between resistant strain and isogenic wild type will do. However, I think illumina sequencing is better for this. 454 is just too error-prone for SNP and mutation detection.
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