User: dllopezr
dllopezr • 30
- Reputation:
- 30
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- New User
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- 1 day, 20 hours ago
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- 10 months, 2 weeks ago
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Posts by dllopezr
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4
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2
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96
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... 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' ...
0
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1
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113
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1
answers
... 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
dllopezr • 30
3
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1
answer
113
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1
answer
... 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 ...
written 4 days ago by
dllopezr • 30
• updated
4 days ago by
Kevin Blighe ♦ 30k
1
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0
answers
112
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0
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... 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 ...
written 8 days ago by
dllopezr • 30
3
votes
1
answer
127
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1
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... 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 ...
written 14 days ago by
dllopezr • 30
2
votes
0
answers
161
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0
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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 9 weeks ago by
dllopezr • 30
• updated
9 weeks ago by
Vijay Lakhujani ♦ 3.1k
2
votes
0
answers
152
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0
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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 10 weeks ago by
dllopezr • 30
0
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2
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468
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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 11 weeks ago by
dllopezr • 30
1
vote
1
answer
122
views
5 follow
1
answer
... 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 11 weeks ago by
dllopezr • 30
• updated
11 weeks ago by
shenwei356 ♦ 4.2k
2
votes
2
answers
271
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2
answers
... 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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