User: Fatima

gravatar for Fatima
Fatima930
Reputation:
930
Status:
Trusted
Location:
United states
Website:
https://homes.luddy.in...
Twitter:
fsharifi4
Scholar ID:
Google Scholar Page
Last seen:
17 hours ago
Joined:
4 years, 3 months ago
Email:
f************@gmail.com

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 >
0
votes
0
answers
123
views
0
answers
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 Fatima930
0
votes
0
answers
123
views
0
answers
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 Fatima930
0
votes
1
answer
280
views
1
answers
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 Fatima930
0
votes
1
answer
107
views
1
answers
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 Fatima930
0
votes
1
answer
107
views
1
answers
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 Fatima930
2
votes
0
answers
107
views
0
answers
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 Fatima930
0
votes
5
answers
145
views
5
answers
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 Fatima930
0
votes
3
answers
148
views
3
answers
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 Fatima930
0
votes
3
answers
148
views
3
answers
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 Fatima930
1
vote
3
answers
148
views
3
answers
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 Fatima930

Latest awards to Fatima

Voter 3 months ago, voted more than 100 times.
Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.
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
Popular Question 4 months ago, created a question with more than 1,000 views. For Samtools depth input
Popular Question 5 months ago, created a question with more than 1,000 views. For Samtools depth input
Scholar 11 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Centurion 12 months ago, created 100 posts.
Scholar 12 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Scholar 13 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Parsing gff files using python and awk
Popular Question 2.9 years ago, created a question with more than 1,000 views. For concatenating different columns of different files bash script
Scholar 3.4 years ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: bash script for RNA seq analysis
Supporter 3.4 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1395 users visited in the last hour
_