I am facing difficulty in running blast sequencing in that software as it takes too much time and it gets terminated automatically after sometime. So anyone knows about it how to resolve it or any other alternative software for genome scale reconstruction?
That is why I normally avoid software packages that integrate other software to make life easier to users. One cannot avoid sometimes the intricateness of life. Well, why not trying the steps by yourself? for example, if you have your genome sequence, then try GeneMark (there are versions for prokaryotic and eukaryotic sequences, depending on your needs). Then avoid BLAST, because that is normally the bottleneck in massive analyses, thus try something like DIAMOND or Lambda aligner for searching protein-coding genes against any protein-sequence database you are comfortable with, let's say UniProt, RefSeq, Kegg, or even NCBI-nr. For RNA sequences you can try Rfam for general RNA, or Silva for rRNA sequences. Then you can use Kegg database to map proteins to metabolisms, etc..
I'm sorry I am not answering your question directly.. just giving alternatives.
Thanks for your response yeah i know few of the things you mentioned and rest of them are good points for knowledge purpose but when you are working with a software and everything corresponds to that for further analysis you can not divert to sub alternatives in such cases. Secondly when you do BLAST and all then those results can not be uploaded in the software so thats a second problem....
I know that.. the problem was made before then, when someone selected a software package that was not properly evaluated for meeting your needs and resources (otherwise you wouldnt be asking this question). Anyway.. for alternatives like those I was pointing out I would be more than happy to help.
Best of luck
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