User: Fatima
Fatima • 340
- Reputation:
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- United states
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- http://homes.sice.indi...
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Posts by Fatima
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... I think it's good as it is now. I can delete my responses to you to tidy up. ...
written 3 days ago by
Fatima • 340
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... 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
Fatima • 340
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... 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
Fatima • 340
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... 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
Fatima • 340
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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
Fatima • 340
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... 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
Fatima • 340
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... 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
Fatima • 340
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... 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
Fatima • 340
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... 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
Fatima • 340
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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
Fatima • 340
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