User: Käpt'N Silico

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Posts by Käpt'N Silico

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Comparing Assemblies
... Go for compressed XML output with BLAST. Tabular format used to change and is not supported or recommended by some parsers any more. XML contains all information in a well-defined format and can still be converted to any other format that BLAST can produce. ...
written 7.2 years ago by Käpt'N Silico20
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Comment: C: Default Frameshift Penalty For Blastx
... I will also do this but it would be nicer for any scientific program to document this kind of behavior. ...
written 7.8 years ago by Käpt'N Silico20
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Answer: A: Default Ncbi Blast+ V. 2.2.25 Parameters
... This is a valid question. Even though it is not said in the documentation anywhere, your results should be accompanied by the parameters used. So I ususally use the BLAST XML output format and look through the header. Some parameter values are given there. However, I cannot find any frameshift penal ...
written 7.8 years ago by Käpt'N Silico20
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Default Frameshift Penalty For Blastx
... I do not set the frameshift penalty costs and output everything in BLAST XML format. Then I go through this file and usually the beginning contains parameters of the scoring scheme etc. But it does not contain any entry about frameshift costs. Does anybody know about this? Are frameshifts allowed at ...
blast written 7.8 years ago by Käpt'N Silico20 • updated 7.8 years ago by Larry_Parnell16k
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Comment: C: Refseq Genbank To Fasta Format Failing With Contig Fields
... I checked with the NCBI and they told me that this is intended and you are supposed to download both, FASTA and Genbank files. ...
written 7.9 years ago by Käpt'N Silico20
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Comment: C: Refseq Genbank To Fasta Format Failing With Contig Fields
... Yes thanks, I know there are FASTA files which I already downloaded. This question was rather one of principle. I hate to download both, GenBank and FASTA to get sequence and annotation information. If it is not possible to convert GenBank to FASTA offline, there is no sense in providing two formats ...
written 8.0 years ago by Käpt'N Silico20
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Comment: C: Refseq Genbank To Fasta Format Failing With Contig Fields
... Thanks, I made the data issue a little clearer. This happens with the official RefSeq release 47. My thinking was that is would be self-contained and thus be able to flatten the files in order to contain no sequence references any more without additional data. ...
written 8.0 years ago by Käpt'N Silico20
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Refseq Genbank To Fasta Format Failing With Contig Fields
... I used to generate FASTA out of my GenBank source files using a simple conversion script: #!/usr/bin/env python from Bio import SeqIO def wrap( text, width=80 ): for i in xrange( 0, len( text ), width ): yield text[i:i+width] if __name__ == "__main__": status = progress() for record in Seq ...
refseq biopython genbank written 8.0 years ago by Käpt'N Silico20 • updated 7.9 years ago by Peter5.8k

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