User: shirani.s

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shirani.s10
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Posts by shirani.s

<prev • 7 results • page 1 of 1 • next >
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MAFFT branch length VS. BLAST
... I am trying to compare 10 sequences (~1Mbp size each) to find out their divergence and phylo genetic tree. I am getting my phylo tree from MAFFT which provides the branch length in "substitution per site" unit. However, these branch lengths are by a factor of 10 higher than my results from pairwise ...
mafft blast written 2.5 years ago by shirani.s10 • updated 2.2 years ago by pawlowac60
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Comment: C: ClustalO input file
... Although there is no specification of the length of the alignment, I cut it short to ~800bp and it worked. ...
written 2.9 years ago by shirani.s10
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ClustalO input file
... I am trying to use clustalO for Multiple Sequence Alignment on some synthetic genome files I created in fasta format but neither the web application nor the command line version accepts the input (ERROR: Cannot open input file. No alignment!). My sequences are 5000bp in length (all the same length) ...
clustalo fasta msa written 2.9 years ago by shirani.s10
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Bio::Phylo tree drawer text
... I am using a perl script to draw a Newick format tree using Bio::Phylo::Treedrawer. Here's the related part of the code: $newickString .= ';'; my $forest = Bio::Phylo::IO->parse( -format => 'newick', -string => $newickString ); my $tree = $forest->f ...
bio::phylo tree written 3.0 years ago by shirani.s10 • updated 3.0 years ago by genomax65k
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Comment: C: Unexpected BLAST results
... Thanks, this helped a lot. I used `-qcov_hsp_perc`100 here and worked fine for mine. I'm just going to explain further below for future reference. The problem in my output was that it is aligning genes in the middle of the alignment as well as the whole query. I needed a command to filter BLASTn o ...
written 3.0 years ago by shirani.s10
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Comment: C: Unexpected BLAST results
... - Aren't are the e-value s 0.00 in the above output? Could you explain a bit more? - If this is the case, how come it works on other shorter alignments but not this one? ...
written 3.0 years ago by shirani.s10
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Unexpected BLAST results
... I'm using this blastn command to find identity between a number of sequences. This is the command: blastn -query IAM_O_DNA_0001_0001.txt -subject IAM_O_DNA_0001_0001.txt -outfmt 10 -max_target_seqs 100000 1>BLAST_O_0001_0001.txt I'm basically blasting the same file against itself. The file ...
nucleotide blastn output written 3.0 years ago by shirani.s10 • updated 3.0 years ago by h.mon24k

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