User: BiomedicalTissueIng

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Posts by BiomedicalTissueIng

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What could be a good strategy to describe GO enrichments for a pubblication?
... Hi guys, I am studying M.musculus proteins using a certain operational classification that allows me to divide the entire proteome into 3 categories. Using g: profiler I observed that the GO terms relating to BP, MF and CC have almost no intersections in the three categories therefore, calling them ...
go written 2 days ago by BiomedicalTissueIng20
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How to Interpret Author's Methods in this article?
... I have to reproduce a result for school reasons (bioinformatics exam) and I was assigned a certain article. In particular I have to reproduce what some authors did in: doi: 10.1371 / journal.pone.0217889. From what I understand, they make functional enrichments in respect of three variants of protei ...
go written 12 days ago by BiomedicalTissueIng20
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Comment: C: Very strange duplicate output with stand alone blast
... I have tried -max_hsps 1 but it remains with similar problems even if not so such aggravated ...
written 14 days ago by BiomedicalTissueIng20
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Very strange duplicate output with stand alone blast
... Hi I'm using stand alone blastn. I got a strange output with duplicated data. If it were for multiple association with different protein ID it would have not been a problem since it could have had a biological meaning. However, it is not the case. Let me use ProtORG1_1...ProtORG1_N to denote the IDs ...
blast written 14 days ago by BiomedicalTissueIng20
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Comment: C: Question : How to read this kind of Stand Alone BLAST Formatted File?
... From what I read from https://open.oregonstate.education/computationalbiology/chapter/command-line-blast/ the Pairwise output is not parseable . Is it correct? ...
written 4 weeks ago by BiomedicalTissueIng20
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Comment: C: Question : How to read this kind of Stand Alone BLAST Formatted File?
... Yes I know for output. So it is a SAM output that is returned. I'll try with MATLAB samread and see what comes out! ...
written 4 weeks ago by BiomedicalTissueIng20
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Comment: C: Question : How to read this kind of Stand Alone BLAST Formatted File?
... For example, if I take the MATLAB swalign (https://it.mathworks.com/help/bioinfo/ref/swalign.html) function this returns me a structure where for each alignment I have, separated, the scores and the alignment. I would like to understand what kind of format this is returned to me in order to choose a ...
written 4 weeks ago by BiomedicalTissueIng20
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Question : How to read this kind of Stand Alone BLAST Formatted File?
... I constructed this type of file by making an alignment between two isolates of the same organism by aligning the protein coding sequences through the following command line with STAND ALONE BLAST: `blastn -query fasta1.fasta -subject fasta2.fasta -dust no -parse_deflines -evalue 1e-10 -max_target_s ...
blast written 4 weeks ago by BiomedicalTissueIng20 • updated 4 weeks ago by lieven.sterck10k
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Comment: C: Why enrichGO does not return any enrichment terms?
... Do you intend to change BH to another kind of test? ...
written 4 weeks ago by BiomedicalTissueIng20
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Comment: C: Why enrichGO does not return any enrichment terms?
... So do you think it is independent from the script? ...
written 4 weeks ago by BiomedicalTissueIng20

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