User: genious.kalia.141198

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Posts by genious.kalia.141198

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Comment: C: How can I Extract PMID only for a query in a text file while searching it on NCB
... thanks for helping me. but I'm getting this error "WebEnv value not found in fetch input" ...
written 4 months ago by genious.kalia.1411980
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How can I Extract PMID only for a query in a text file while searching it on NCBI pubmed?
... Hello all. I have search ***"mycobacterium avium complex"*** at NCBI pubmed and I got **5963** results. I just want to **extract only the PMID** of all these 5963 papers in a file, can be a text file. Is it is possible or not, if possible please help me in doing the same. Thanks. ...
sequence alignment extraction next-gen literature written 4 months ago by genious.kalia.1411980 • updated 4 months ago by genomax69k
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Protein categorization using COG
... Hello all. I have a bacterial genome sequence (size 4.0-7.0) , i need to annotate it according to the 17 categories of COG, can I use COG soft (https://sourceforge.net/projects/cogtriangles/files/) for the same purpose or is there any other method or tool available for doing same. Has anybody co ...
genome gene alignment sequence written 11 months ago by genious.kalia.1411980 • updated 9 months ago by harish200
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Comment: C: Error while using MPI-BLAST
... `yeah, i resolved this.. but MPI-BLAST still generating errors.` mpiexec -n 3 mpiblast -p blastn -d mpiblast/all_ASM.fna -i /home/ntm/samples/test_data/100/100.fasta -o /home/ntm/samples/test_data/100/r_100.txt [blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fna.000.nin [blas ...
written 12 months ago by genious.kalia.1411980
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Comment: C: Error while using MPI-BLAST
... yes, i did. just after my formatted database get ready i copied all the files to the location you mentioned. ...
written 12 months ago by genious.kalia.1411980
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Error while using MPI-BLAST
... I installed MPI-BLAST in linux (ubuntu 16.04) , but while running query its generates an error, which may be pointed towards DATABASE. **to create database i ran this query:** $mpiformatdb -N 16 -i /home/ntm/Downloads/MPI_BLAST_MTB_ASM/all_ASM.fna -o /home/ntm/mpiblast/mtb_ASM **result was:** ...
genome software error alignment sequencing written 12 months ago by genious.kalia.1411980 • updated 12 months ago by Sej Modha4.2k
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Comment: C: How can I add an incremented value just after Accession no. ?
... i think seqkit is not installed thats why generating error. command not found. ...
written 12 months ago by genious.kalia.1411980
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Comment: C: How can I add an incremented value just after Accession no. ?
... thank you so much it works.. ...
written 12 months ago by genious.kalia.1411980
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How can I add an incremented value just after Accession no. ?
... I have a **large csv file (1.7GB) containing sequences,** and i have to provide a **header to each sequence**, so i did some thing like this with bash to do same: ***#/bin/bash cat con_test.csv > out.out for file in out.out; do sed -e 's/^/>NZ_CP00000.1 volvox complete genome\n/' -i ...
genome assembly alignment written 12 months ago by genious.kalia.1411980 • updated 12 months ago by cpad011211k

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