User: Fatima

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Fatima340
Reputation:
340
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Location:
United states
Website:
http://homes.sice.indi...
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fsharifi4
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Last seen:
2 hours ago
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3 years, 2 months ago
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Posts by Fatima

<prev • 114 results • page 1 of 12 • next >
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Comment: C: Finding gene matches using sequence reads?
... I think it's good as it is now. I can delete my responses to you to tidy up. ...
written 3 days ago by Fatima340
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Comment: C: Finding gene matches using sequence reads?
... I fixed it, I'm sorry I was using my phone, and I meant to post it as a comment in response to @anabaena, but I don't know why it was posted as an answer. ...
written 3 days ago by Fatima340
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Comment: A: Finding gene matches using sequence reads?
... You don't need to use the whole pipeline (Fun4me) . You can just use Fraggenescan to predict the gene sequences and then use blast. Please see the last line of this link (examples of Fraggenescan results using metagenomes as input): https://omics.informatics.indiana.edu/FragGeneScan/result.php I ...
written 3 days ago by Fatima340
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Comment: A: Finding gene matches using sequence reads?
... It might be a good idea to assemble the reads and use a tool like Fraggenescan (it's really fast) to predict the gene sequences and then you can use blast to search them against your genes of interest. The following pipeline might give you some ideas: https://experiments.springernature.com/articl ...
written 4 days ago by Fatima340
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Comment: C: Short protein sequence alignment
... I'm not sure about pairwise alignments but for multiple sequence alignment you can use MAFFT and then guidance Please see the output of guidance: http://guidance.tau.ac.il/results/15816469509376/MSA.MAFFT.Guidance_res_pair_res.html GUIDANCE alignment score: 0.306977 This article might help: ...
written 4 days ago by Fatima340
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Comment: C: How can I extract position information from multiple alignment format?
... I don't think MAFFT works well for pairwise alignment. I think you can try local or global alignment tools or blast. And if you have a set of reads and a reference you can try bowtie2. But if you want to parse your current output hopefully there's a tool oit there but if you want to write your o ...
written 4 days ago by Fatima340
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Comment: C: Using Entrez to find the taxonomy for an accession number
... Would it work if you add the possible dbs to a file (db.list) each db in one line and use something like this? cat db.list | while read line ; do esearch -db ${line} -query "WP_003131952.1" | elink -target taxonomy | efetch -format native -mode xml | grep ScientificName | awk -F ">|<" ' ...
written 4 days ago by Fatima340
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Comment: C: The genotype imputation in Beagle always stop on specific step and can not finis
... These links might help: https://www.biostars.org/p/292635/ https://faculty.washington.edu/browning/beagle/beagle_5.0_14May18.pdf Are there NaN's in your data? ...
written 4 days ago by Fatima340
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Answer: C: How to generate sequence length distribution from Fasta file
... You can use a script like this to find the lengths cat file.fa | awk '$0 ~ ">" {print c; c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' https://www.danielecook.com/generate-fasta-sequence-lengths/ And this script should give you length and count ...
written 4 days ago by Fatima340
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Comment: C: Short protein sequence alignment
... >query SDPLSMVGPSQGRSPSYAS >subject1 VNTHAGGTGPEGCRPFAKF >subject2 HLESDMFSSPLETDSMDPF If your sequences were longer you could use blastp (Align two or more sequences option). MAFFT output id1 -------SDPLSMVGPSQGRSPSYAS id3 ...
written 4 days ago by Fatima340

Latest awards to Fatima

Centurion 5 days ago, created 100 posts.
Scholar 8 days ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Scholar 15 days ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Popular Question 22 months ago, created a question with more than 1,000 views. For Parsing gff files using python and awk
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Scholar 2.4 years ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
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