User: saladi1

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saladi130
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Posts by saladi1

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Paired-end reads that span a position in an assembly
... I need to find pairs of reads that *span* a certain position in an assembly. However, neither needs to necessarily correspond to that position. To be clear, here is an example: assembly: ----------------------[=====================]---------------------------- pair A: -----[<< ...
bedtools genome paired-end assembly written 6 days ago by saladi130 • updated 6 days ago by Pierre Lindenbaum122k
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Answer: A: How To Make A .Free Format Sequence Alignment File (For Matlab) ?
... Old post, but for those who get here in the future, one alternative is to use the [multialignread][1] function in the bioinformatics toolbox with a ClustalW, GCG, or PHYLIP formatted alignment: [labels,seqs]=multialignread(filename); labels=char(labels); seqs=char(seqs); [1]: http ...
written 22 months ago by saladi130
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Comment: C: Help To Blast Sequences Against Drosophila Genome In Biopython
... Perhaps there has been a change since on NCBI's side since this posting, but the correct way to do this would be through the "entrez_query" argument: NCBIWWW.qblast(program="blastn", database="refseq_genomic", sequence=input_sequence, entrez_query="txid7227[ORGN]") ...
written 4.0 years ago by saladi130
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Comment: C: BLAST via Biopython NCBIWWW. Where can I find the complete database list?
... For future readers that happen upon this page, the correct entrez query to specify sequences from taxid 9606 is "txid9606[ORGN]" Perhaps this is a change on NCBI's side since the previous comment.  ...
written 4.0 years ago by saladi130
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Answer: A: What "column weight" really means in RaXML?
... For those looking for the response from the mailing list: "that is correct, but a weight of 9 essentially means that you are  replicating that site 9 times in the alignment,  alexis" https://groups.google.com/forum/#!topic/raxml/Hfpl1cNKxp8 ...
written 4.1 years ago by saladi130

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