User: arriyaz.nstu

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Posts by arriyaz.nstu

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Comment: C: How to fetch a nucleotide sequence of a certain CDS from linux terminal by using
... You made my day. Thank you very much. ...
written 8 days ago by arriyaz.nstu0
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Comment: C: How to fetch a nucleotide sequence of a certain CDS from linux terminal by using
... Hi, your code is just amazing. Thank you very much. Is it possible to download the CDS from more than one accession together in a single code? Becuase I have a very long list of accession numbers and I've to download CDS of ORF57 for all of them. ...
written 8 days ago by arriyaz.nstu0
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How to fetch a nucleotide sequence of a certain CDS from linux terminal by using GenBank accession number.
... Let's say, I have two accession numbers **AP017458** & **GQ994935** of a virus's GenBank file. I want to download the nucleotide sequence (CDS) of ORF57 from these accession from Linux terminal. As per as I know **efetch**, **esearch**, etc command line code can be used to download sequence dire ...
gene sequence written 8 days ago by arriyaz.nstu0 • updated 8 days ago by genomax84k
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Comment: C: How to extract certain CDS from a GenBank file in linux terminal
... Thank you for your code. I run the code according to your instruction. But, it generating all amino acid sequences for every CDS. But my target is to get DNA sequence of a specific CDS (lets say, ORF4). ...
written 8 days ago by arriyaz.nstu0
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Comment: C: How to extract certain CDS from a GenBank file in linux terminal
... **Okay, according to your suggestion I cut off some portion of these genbank records. Here, there are two genbank record in a single file:** LOCUS MK733608 136382 bp DNA linear VRL 13-MAY-2020 DEFINITION Human gammaherpesvirus 8 strain UNC_KICS010, complete geno ...
written 8 days ago by arriyaz.nstu0
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Comment: C: How to extract certain CDS from a GenBank file in linux terminal
... Here I don't find any option to upload the GenBank file. But it is very long file, so do I just copy-paste it here? ...
written 8 days ago by arriyaz.nstu0
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How to extract certain CDS from a GenBank file in linux terminal
... Hi, I have a large GenBank file that contains multiple records. I got this file after performing BLAST against my query sequence. This .gb file contains all the results (full record in GenBank format for each accession) from the blast search. I want to extract a certain CDS from each record in that ...
gene genome sequence written 8 days ago by arriyaz.nstu0
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How to check the conservancy of DNA sequence.
... I have a small DNA segment and my dataset has almost 100 long DNA sequences. I want to **check whether this DNA segment is conserved among all DNA sequences in my dataset**. The conservancy result should be in a percentage (like it is 90% or 100% conserved). [IEDB Epitope Conservancy Analysis tool][ ...
conservancy dna written 7 weeks ago by arriyaz.nstu0
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Comment: C: Sort and extract common entries from a txt file.
... After running the final code, I am getting the following error $ join -1 1 -2 1 -o 1.1,1.2,1.3,2.2,2.3 data.txt <(join -1 1 -2 2 colA.txt colB.txt | tr " " "\t") | tr " " "\t" >> result.txt join: colB.txt:2: is not sorted: 663 77.5 join: colA.txt:5: is not sorted: 1067 0.873 ...
written 7 weeks ago by arriyaz.nstu0
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Comment: C: Sort and extract common entries from a txt file.
... I removed the post from stackexchange. ...
written 7 weeks ago by arriyaz.nstu0

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