User: dllopezr
dllopezr • 20
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Posts by dllopezr
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... 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 ...
written 4 days ago by
dllopezr • 20
• updated
4 days ago by
Vijay Lakhujani ♦ 3.0k
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... 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 ...
written 6 days ago by
dllopezr • 20
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... 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
dllopezr • 20
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5 follow
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... 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 ...
written 15 days ago by
dllopezr • 20
• updated
15 days ago by
shenwei356 ♦ 4.1k
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... 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!! ...
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... 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
dllopezr • 20
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... 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
dllopezr • 20
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... Thanks genomax and lieven.sterck. But didn't work, the output is the same.
...
written 9 weeks ago by
dllopezr • 20
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... 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
dllopezr • 20
2
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... 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 ...
written 9 weeks ago by
dllopezr • 20
• updated
9 weeks ago by
WouterDeCoster ♦ 31k
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