Can you suggest a tool that accepts Whole genome Multiple contig DNA sequences in multiFASTA format for whole genome analysis for putative PKS/NRPS gene clusters.
This should do the job http://antismash.secondarymetabolites.org/
I have used antiSMASH for analysis, will you suggest another toll which accept genomic input in MultiFASTA format.. most of the tools like SMURF, ASMPKS, SEARCHPKS, NRPSpredictor are required protein sequence it is so become very difficult to analyse whole genome protein sequence for putative secondary metabolite gene clusters....
can you try gene prediction to obtain putative protein sequences and then use the tools mentioned in your reply?
i have tried Gene mark for gene prediction it has predicted > 6000 genes and their corresponding protein sequence ...it is huge task to analyze all protein sequences for putative bio-synthetic gene clusters by any tools b'coz all are accepting single polypeptide sequence.... in not more than 10 tabs that's why we are only able to analyse max 10 polypeptide Sequence at a time..
If you have predicted protein sequences than a pfam or HMM scan can get you your results? or a CDD blast? ... Here I am now assuming you want to see which predicted proteins have homology with PKS/NRPS.
Also have a look at this publication (http://www.nature.com/ja/journal/v67/n1/full/ja2013125a.html) and this (http://www.sciencedirect.com/science/article/pii/S0944501304000801) and may be this too (http://www.biomedcentral.com/1471-2105/9/454)
try the list here, may be u can find one for your use,
http://www.secondarymetabolites.org/mining/
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