User: radha.jg

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radha.jg0
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Posts by radha.jg

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Comment: C: Command line argument error: Argument "query". File is not accessible: `psitmp2
... No, the issue isn't the permissions, I have the right ones on the folder I'm running my stuff and the folder where the software was installed. Anyway, I've tried a few things and triggered another error: it seems it doesn't find makemat (is supposedly included in the blast2 package installation, wh ...
written 5 months ago by radha.jg0
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Comment: C: Command line argument error: Argument "query". File is not accessible: `psitmp2
... Where does it save the temporary dir for me to check that? ...
written 5 months ago by radha.jg0
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Command line argument error: Argument "query". File is not accessible: `psitmp24348007f0101.fasta'
... Hello all: I'm using psipred as follows: runpsipred myfile.fasta But it returns this error Command line argument error: Argument "query". File is not accessible: `psitmp24348007f0101.fasta' Also I've downloded the uniprot files on the server and decompresed in multiple files: ls un ...
sequence psipred written 5 months ago by radha.jg0
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Comment: C: Can anyone reccomend me a software predictor of secondary structures from aminoa
... Does SWISS-MODEL accept a non aligned multifasta, or just a sequence per upload? ...
written 5 months ago by radha.jg0
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Comment: C: Can anyone reccomend me a software predictor of secondary structures from aminoa
... Thanks for the recommendation. I'll check what it can do ...
written 5 months ago by radha.jg0
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Can anyone reccomend me a software predictor of secondary structures from aminoacid sequence
... Hello all I have a multifasta with the protein sequences of an organism and I want to obtain a tsble of predictions of secondary structures similar to the output of TMHMM (http://www.cbs.dtu.dk/services/TMHMM/). The problem with TMHMM is that it only predicts alpha-helixes because it assumes all the ...
sequence proteins written 5 months ago by radha.jg0 • updated 5 months ago by Kevin Blighe66k
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Comment: C: How can I parse GFF3 using BCBio?
... Yes, I saw that, so now what I need to do is to, get a list of genes for one seqid (salida parameter), from the gff3 database. Then construct a list of tuples for each gene and then, add that data to the plot... Mmm I really need to meditate how to do this EDIT: ok, thing is, I just have the chromo ...
written 9 months ago by radha.jg0
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Comment: C: How can I parse GFF3 using BCBio?
... Ok, so now what I need is an iterator to get all CDS with all start, end and and strand for a chromosome. Does this library provide one, or how do I get this. Context: For each chromosome I calculated the GC_Skew and now I need to show in that plot, the zones that have CDS, distinguishing the zones ...
written 9 months ago by radha.jg0
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How can I parse GFF3 using BCBio?
... I have the following code: import sys from BCBio import GFF file = sys.argv[1] for record in GFF.parse(file): print([record.seqid,record.source, record.start, record.end, record.strand]) My question is how can extract the ids, the chromosome, the coordinates and the stran ...
biopython written 9 months ago by radha.jg0 • updated 7 months ago by Biostar ♦♦ 20
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Is there a program better than CodonW for CAI?
... Hi. I'm searching for a tool better than codonW because the .out it gives me is an empty file, gives a warning to the mayority of my secuences, adn I want to calculate apart from CAI, %minmax and absolute rareness. Someone can point me in the right direction pleas. ...
sequence written 5.4 years ago by radha.jg0 • updated 5.4 years ago by 5heikki9.0k

Latest awards to radha.jg

Popular Question 5.4 years ago, created a question with more than 1,000 views. For Is there a program better than CodonW for CAI?
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Exclude non coding sequences from multifasta
Popular Question 5.4 years ago, created a question with more than 1,000 views. For make fasta sequences names short
Scholar 5.4 years ago, created an answer that has been accepted. For A: Exclude non coding sequences from multifasta

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