User: saadleeshehreen

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Posts by saadleeshehreen

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Comment: C: How to join multiple files in shell with variable lines?
... Thanks..served my purpose. ...
written 9 days ago by saadleeshehreen70
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How to join multiple files in shell with variable lines?
... Hi, I have 10 .txt files. Each of them have one column with variable lines. For example, file 1 has 92, file 2 has 103 lines. The content of one file is as below. Aca10 AcrIC6 AcrIC7 AcrIE1 AcrIE3 AcrIE9 AcrIF1 AcrIF12 AcrIF16 AcrIF17.1 How to join 10 .txt ...
shell written 9 days ago by saadleeshehreen70
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Answer: A: How to add file name after > in a multi-fasta file?
... `awk '/>/{sub(">","&"FILENAME"_");sub(/\.fasta/,x)}1' sample_1.fasta` ...
written 5 months ago by saadleeshehreen70 • updated 5 months ago by lakhujanivijay5.3k
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How to add file name after > in a multi-fasta file?
... Hi, I have a multi-fastafile called HTH_7.fasta. >W1DFQ1_KLEPN/141-185 GRKKSLSSERIAELRQRVEAGEQKTKLAREFGISRETLYQYLRTD >HIN_SALAE/139-183 GHPRAINRHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPAS >GIN_BPMU/138-182 GRPPKLTKAEWEQAGRLLAQGIPRKQVALIYDVALSTLYKKHPAK >CIN_BPP1/1 ...
fasta rename sequence header written 5 months ago by saadleeshehreen70 • updated 5 months ago by Hugo290
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Download pfam sequence
... Hi, Does anyone know how to download only seed sequence from a pfam clan? This HTH clan has 340 seeds and I want to download only seeds not all sequences. And, need to download .fasta sequence rather alignment. https://pfam.xfam.org/clan/HTH#tabview=tab2 Thanks in advance. Cheers ...
sequence written 6 months ago by saadleeshehreen70 • updated 6 months ago by Mensur Dlakic7.0k
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Comment: C: getting information from NCBI genebank files
... It could be any protein associated with anti-restriction. I am looking for a correlation between 'protein A' with anti-restriction proteins. I have already got 600 genomes having protein A. Now, trying to look at which of these genomes have anti-restriction proteins. ...
written 8 months ago by saadleeshehreen70
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getting information from NCBI genebank files
... Hi, I am interested to know about the presence of a specific protein called "anti restriction" in a list of ~600 genomes of different species of bacteria. It can be find from the NCBI genebank files. Manually checking those 600 genomes is time-consuming. Any suggestions on how can I know which of th ...
ncbi assembly genebank annotation written 8 months ago by saadleeshehreen70
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How to extract a particular region from a nucleotide contig?
... Hi, I have downloaded a contig from NCBI. It is around 100 kbp long and has a integrated prophage region. The prophage region is between 54501-90604 bp. How to extract only 54501-90604 bp from this contig? Cheers ...
assembly sequence written 11 months ago by saadleeshehreen70 • updated 11 months ago by Pierre Lindenbaum131k
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Retrieving organism name
... Hi, I usually use the following command to get GCF_id (Accession) from the NCBI. How Can I retrieve the "organism name/source" from NCBI? cat NZ_id.txt | while read i; do elink -db nuccore -id $i -target assembly|esummary| xtract -pattern DocumentSummary -element AssemblyAccession ; done ...
ncbi assembly e-utlilities written 16 months ago by saadleeshehreen70 • updated 16 months ago by AK1.9k
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How to Deduplicate files
... Hi, I have list of 160111 protein files. Some of the files are duplication as GCA and GCF id contains same protein sequnces. How I can deduplicate the list on the basis of ASM102201v1? Enterobacter_hormaechei-158836#GCA_001022015.1/GCA_001022015.1_ASM102201v1_protein.faa Enterobacte ...
sequence written 18 months ago by saadleeshehreen70 • updated 18 months ago by finswimmer13k

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