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User: Fatima

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Fatima • 930
Reputation:
930
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Trusted
Location:
United states
Website:
https://homes.luddy.in...
Twitter:
fsharifi4
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Last seen:
17 hours ago
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4 years, 3 months ago
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Bioinformatics Discord

myRT  (RT Identification/Classification)

Fun4me (Functional Annotation for Metagenomes)

myDGR (Identification of DGR systems)

FragGeneScan (Gene Predictor)

PROPER (Performance visualization in MATLAB)


 

 

Posts by Fatima

<prev • 282 results • page 1 of 29 • next >
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Comment: C: Plot phylogenetic tree with all ancestor nodes
... Please try uploading your file to ITOL and see if you get a different result (it's easy to use): https://itol.embl.de/upload.cgi Could you tell me the accession number of the ancestor node? ...
written 3 days ago by Fatima • 930
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Comment: C: Plot phylogenetic tree with all ancestor nodes
... Hi! Have you tried these packages? You may want to give them a try. https://cran.r-project.org/web/packages/castor/index.html https://guangchuangyu.github.io/software/treeio/ ...
written 5 days ago by Fatima • 930
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Comment: C: How to download a list of all KEGG orthologs with respect to KEGG module (or pat
... Can you use MetaCyc instead? https://biodatamining.biomedcentral.com/articles/10.1186/s13040-018-0166-8 See data/pathways.info https://sourceforge.net/p/fun4me/code/ci/master/tree/ ...
written 10 days ago by Fatima • 930
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Comment: C: Retrieving all genes associated with a GO term
... Have you tried changing the headers of the files (go_id to go), and then get the list of attributes? The link to the post in your original question doesn't work. Are you referring to this post? https://www.biostars.org/p/354675/ Another good resource: https://www.stat.berkeley.edu/~sandrine/ ...
written 23 days ago by Fatima • 930
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Comment: C: Retrieving all genes associated with a GO term
... I think "filters" should match with attributes and headers of the data. So, if you're using "go" as filters, the header and attribute should also be "go" instead of "go_id", or you can use filters="go_id" to match. ...
written 23 days ago by Fatima • 930
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Comment: C: WGS Metagenomics mapping for functional annotation (KEGG/ other database)?
... Hi, you can use `metaCyc`. Check `Fun4me` for more information. https://link.springer.com/protocol/10.1007/978-1-4939-7015-5_3 https://sourceforge.net/projects/fun4me/ ...
written 27 days ago by Fatima • 930
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Answer: C: Split multifasta-file into multiple files according to a pattern in header
... If your sequences are one and only one line you can use: grep -A 1 ";partial=00;" file > file1 grep -A 1 -E ";partial=01;|;partial=10;|;partial=11;" file > file2 If your sequences occupy more that one line, you can use this command to convert your sequences: awk '/^>/ { ...
written 27 days ago by Fatima • 930
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Comment: C: How to extract fasta headers that contains specific text and it's sequence
... Are the headers exactly identical? grep "16S_rRNA" filename > headers #This is not very efficient but should do the work cat headers | sort | uniq | while read line ; do grep -A 1 "${line}" filename >> output ; done ...
written 28 days ago by Fatima • 930
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Comment: C: How to extract fasta headers that contains specific text and it's sequence
... You can use cd-hit with cutoff value of 1 (-c 1), it will remove the redundant sequences, but will also remove them if their header is different (as long as sequences are identical). So, for example when you have three identical sequences, the output file will only contain one of them ( the represen ...
written 29 days ago by Fatima • 930
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Answer: C: How to extract fasta headers that contains specific text and it's sequence
... If each sequence is **one and only one line:** grep -A 1 "16S_rRNA:" filename Should do the trick! ...
written 29 days ago by Fatima • 930

Latest awards to Fatima

Voter 3 months ago, voted more than 100 times.
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Scholar 4 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: bash script for RNA seq analysis
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Scholar 11 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
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Scholar 12 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
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