User: nvijay.1991

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Posts by nvijay.1991

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Comment: C: Biopython xml parser for psiblast outputs
... Thnak you Peter.. ...
written 3.1 years ago by nvijay.19910
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Jackhmmer domtbl output with iteration information
... At present I am running Jackhmmer for N=5 (5 iterations), which gives me only one domtbl final output after 5th iteration. But, I like to get hits for each iteration (five domtbl outputs or else single domtbl containing iteration information) . Any other suggestions are most welcomed. Thanks in ad ...
jackhmmer written 3.1 years ago by nvijay.19910 • updated 3.0 years ago by Biostar ♦♦ 20
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Biopython xml parser for psiblast outputs
... HI all, I am wondering that, is there any way to parse the PSIBLAST output at each iteration and check for the hits conservation and if condition get satisfied then only perform next iteration. For example: iteration 1 : hit1; hit2; hit3; hit4 case1: hits from iteration 1 are conserved - proceed ...
biopython xmlparser written 3.2 years ago by nvijay.19910
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Comment: C: Biopython: renaming SeqRecords using dictionary values
... from Bio import SeqIO Import deepcopy handle = open('file1', "r") Handle2 =open('file2',"rU') For each_line in handle: ***storing in dictionary goes here*** Suppose dictionary is Id_mapper for record in SeqIO.parse(handle, "clustal") : Record_mod = deepcopy(record) Record_mod.id = ...
written 3.3 years ago by nvijay.19910
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Biopython hmmscan parser
... Hello everyone, I have a hmmscan output in hmmscan3-domtab format with more then 10000 queries. I want to filter each profile hit based on hit_coverage (hmm profile coverage). I was scanning  queryresult--> Hits -->Hsps --> HSPfragment this iterations and calculating hit_coverage then wr ...
searchio biopython hmmscan written 3.4 years ago by nvijay.19910 • updated 23 months ago by O.rka80
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Answer: A: BioPython meme.read MEME output
... I think the length in the file is float,which is supposed to be integer. int('55063.000000') Traceback (most recent call last): File "<stdin>", line 1, in <module> ValueError: invalid literal for int() with base 10: '55063.000000' ...
written 3.6 years ago by nvijay.19910
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Bio.Blast and Blast version compatability
... I am trying to use Bio.Blast for parsing my blast output..but biopoython-1.65 says the Bio.Blast is going to be deprecated and replaced by Bio.SearchIO. since I have Blast output in Plain-text format..I am trying to use  BlastParser and PsiblastParser included in Bio.Blast.NCBIStandalone module. I ...
biopython blast bio.blast written 3.7 years ago by nvijay.19910 • updated 3.4 years ago by Peter5.8k
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how can we obtain protein-based confidence for protein ID and probabilities for differential expression..?
... how can we obtain  protein-based confidence for protein ID and probabilities for differential expression..? for protein id's obtained by itraq analysis( ms/ms) ...
confidence expression protein id written 4.2 years ago by nvijay.19910 • updated 3.2 years ago by Biostar ♦♦ 20
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Answer: A: Retrieving Gene Expression Profiles For A Set Of Genes From All Tissues?
... In similar way,how can i retrieve the information for differential expression analysis for protein accession id's generated through itraq ms/ms method.and how can we achieve the confidence of obtained id's/intensity values..? ...
written 4.2 years ago by nvijay.19910

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