User: Sej Modha

gravatar for Sej Modha
Sej Modha2.6k
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2,590
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Glasgow, UK
Website:
http://bioinformatics....
Twitter:
SejModha
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36 minutes ago
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4 years, 2 months ago
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Posts by Sej Modha

<prev • 406 results • page 1 of 41 • next >
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Answer: C: Retrieve sequences that generated a HMM profile
... I do not think it is possible to get those sequences as HMM algorithm does not save them, however, you can use hmmemit as you mentioned. It is possible to tweak the hmmemit parameters to match the profile. Please refer to the [HMMER documentation.][1] [1]: http://eddylab.org/software/hmmer3/3.1 ...
written 21 hours ago by Sej Modha2.6k
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Comment: C: 1D^2: Oxford nanopre technology
... I guess [SEQanswers][1] or [ONT-community][2] would be a better place for this question. You could also try Twitter! [1]: http://seqanswers.com/ [2]: https://nanoporetech.com/community ...
written 21 hours ago by Sej Modha2.6k
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Comment: C: Extracting specific IDs + sequence from multifasta
... What do you mean by > So between each ID and sequence is a new line. Do you mean empty new line? If the sequences do not contain new line character (i.e. are not folded) then you can try: grep -A1 "[gene1]" input.fasta > output.fasta ...
written 1 day ago by Sej Modha2.6k
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Comment: C: Convert Nexus format to Newick format
... Does it have to be a Perl module or you could try [BioPython][1] Phylo.convert instead? [1]: http://biopython.org/wiki/Phylo ...
written 2 days ago by Sej Modha2.6k
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Comment: C: Has anyone used Circa to plot MBD-seq data?
... Do you mean [Circa][1] tool? If yes, then you should maybe have a look at the tutorials on their website or contact the developers directly as it is a commercial tool that not many people would have tried/bought. [1]: http://omgenomics.com/circa/ ...
written 4 days ago by Sej Modha2.6k
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Comment: C: How to keep a log of columns removed from edited MSA?
... Have you tried [Gblocks][1]? [1]: http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html ...
written 4 days ago by Sej Modha2.6k
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Comment: C: Create workflows for behind the scene processes
... Is it possible to build a flowchart using a generic app like [draw.io][1] and then embed that within Shiny? [1]: https://www.draw.io/ ...
written 5 days ago by Sej Modha2.6k
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Answer: C: How to query the taxa IDs/GIs of a kraken database
... `seqid2taxid.map` file in the Kraken DB directory contains the seqID and the taxonomy ID as two columns. If a database was built from scratch then the fasta files should be available in the `library/added/*.fna` in the Kraken DB folder. ...
written 5 days ago by Sej Modha2.6k
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Comment: C: Changing fasta headers in multifasta file
... https://www.biostars.org/p/53212/ ...
written 5 days ago by Sej Modha2.6k
0
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Answer: A: Exact match with query architecture option for local version of HMMER
... I have concluded that this is feature is not available in the current version of the local HMMER tool. ...
written 5 days ago by Sej Modha2.6k

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Scholar 5 days ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
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