User: dllopezr

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dllopezr20
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Posts by dllopezr

<prev • 19 results • page 1 of 2 • next >
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Edit Software to change blast output
... Hi community I am working with a software called **SWeBLAST**, which produce custom subsequences of a fasta format and blast them. The problem is that the blast output of this program by default is the format number `8`, and for my work the query cover parameter is important, so the `blastn` form ...
sweblast python blast written 4 days ago by dllopezr20 • updated 4 days ago by Vijay Lakhujani3.0k
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Kegg Relational Database Access
... Hi community I have a old MySQL version of a Kegg Relational Database For Enzyme and Reactions The Enzyme DB Columns are the EC number, Comments and Description of all Enzymes and The Reaction DB Colums are KEGG_reaction_entry Name Definition Equation and Comment for all reactions There is a way ...
gene database kegg written 6 days ago by dllopezr20
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Comment: C: FASTA file with taxid, want to obtain lineage and put into header
... Hi mariahaguiar001 I have the same challenge of replace by tax full lineage, but I have accesion id´s instead of ncbi taxid, Did you find a not manual way to replace the headers? ...
written 15 days ago by dllopezr20
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Replace Accesion Headers by full ncbi Lineage Taxnomy
... Hi everybody I have several multifasta files with headers like this: >NC_014760.1:c365195-363993 Mycoplasma bovis PG45 clone MU clone A2, complete genome >NC_013511.1:c476217-475021 Mycoplasma hominis ATCC 23114 chromosome complete genome I would like to replace this headers by ncbi ...
gene sequence written 15 days ago by dllopezr20 • updated 15 days ago by shenwei3564.1k
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Command line tool for translated multifasta nucleotide to aminoacid sequence
... Hi everybody I have several multifasta files with nucleotide gene sequences. Could you give me recommendations of command line tools to translated this files to aminoacid sequences in new files with the same title and headers of origin? Thank you!! ...
gene sequence written 15 days ago by dllopezr20 • updated 15 days ago by genomax54k
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Comment: C: Perl script to download gene sequences
... Hi lieven.sterck Yes in excel "Inositol" and "pyrophosphate" and "synthase" are present in the same column, and I translated this to csv or tab file. The header of prueba.txt is: Inositol pyrophosphate synthase Inmovilización Sintesis de polifosfatos NA 16 Thank you for your help ...
written 9 weeks ago by dllopezr20
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Comment: C: Perl script to download gene sequences
... Hi, I only test the script with the first row for now, In this case my $i must be Inositol pyrophosphate synthase, but the script do the query only with inositol, and the fasta created is inositol.fasta. I want the query to be over over the whole name and the file created with the name "Inositol_py ...
written 9 weeks ago by dllopezr20
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Comment: C: Perl script to download gene sequences
... Thanks genomax and lieven.sterck. But didn't work, the output is the same. ...
written 9 weeks ago by dllopezr20
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Comment: C: Perl script to download gene sequences
... Thank you so much! The code work but I forgot to say that my table in excel look like this: Inositol pyrophosphate synthase OtherColumn OtherColumn There are spaces in the firts column, and the code only read the first world "Inositol" I translated the excel table to csv and tab separate f ...
written 9 weeks ago by dllopezr20
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Perl script to download gene sequences
... Hi everyone! This entrez command give me an outpout with the genes sequences of a gen/enzymes for various organism: esearch -db gene -query "glutaminase-asparaginase [Gene/Protein Name] AND (bacteria [orgn] OR fungi [orgn] OR archaea [orgn]) AND alive [prop]" | efetch -format docsum | xtract ...
gene perl sequence ncbi written 9 weeks ago by dllopezr20 • updated 9 weeks ago by WouterDeCoster31k

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