User: dllopezr

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dllopezr30
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10 months, 2 weeks ago
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d*******@unal.edu.co

Posts by dllopezr

<prev • 24 results • page 1 of 3 • next >
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How to include complete labels names in R boxplot
... Hi everyone! I am doing an R BoxPlot of OTU abundance trough different samples, but the labels of the x axes are incomplete: For example, one sample name is T1P1_T2_C-1, but in the plot, the labels show only from the P letter. The code I am using is: boxplot(OTUs[, 2:13], main="Boxplot OTU' ...
boxplot R label written 2 days ago by dllopezr30 • updated 2 days ago by zx87545.4k
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Comment: C: Replace between character and white space using unix sed
... Hi @Kevin, thank you for your help! If you don't mind, could you explain to me how this command works, especially this part `ChrStart\-[0-9]*[[:blank:]]`? What I really want to do is to pass this numbers to different variables, say "ChrStart" = $1 and ChrStop = $2 to pass to another command. The ...
written 4 days ago by dllopezr30
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Replace between character and white space using unix sed
... Hi everyone I have a file like this >NC_003037.1:453555-454448 Sinorhizobium meliloti 1021 plasmid pSymA, complete sequence >NC_007493.2:2279220-2278345 Rhodobacter sphaeroides 2.4.1 chromosome 1, complete sequence >NC_007952.1:1763831-1762950 Paraburkholderia xenovorans LB400 ...
replace sed unix written 4 days ago by dllopezr30 • updated 4 days ago by Kevin Blighe30k
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Entrez Direct to retrieve Protein and Coding sequences from NCBI accesion
... Hi everyone! I have a bunch of fasta files of gene sequences that I download from ncbi trough entrez direct tool. I am wondering if it is posible to obtain the protein and coding sequences of these genes using the accession, that is in this format: `NZ_CP006694.1:1104181-1105143` where the data f ...
ncbi retrieve protein entrez coding sequences written 8 days ago by dllopezr30
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Python script strange behavior
... Hi, community! I am learning python with a book called "Python for Biologist". An exercise is to write a function that calculates the percentage of a residue in a protein sequence and evaluate it with the assert function, and this is my solution: from _future_ import division def Residue_p ...
python script written 14 days ago by dllopezr30
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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 9 weeks ago by dllopezr30 • updated 9 weeks ago by Vijay Lakhujani3.1k
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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 10 weeks ago by dllopezr30
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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 11 weeks ago by dllopezr30
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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 11 weeks ago by dllopezr30 • updated 11 weeks ago by shenwei3564.2k
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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 11 weeks ago by dllopezr30 • updated 11 weeks ago by genomax57k

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