User: biostar

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biostar150
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Posts by biostar

<prev • 26 results • page 2 of 3 • next >
16
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13 follow
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How Do I Align More Than Five Long Dna Scaffolds (Contigs) To The Reference Gene?
... Hi everyone, I tried to align one of my reference genes with its contigs using Mauve, MAFFT, emboss needle etc, but could not get it aligned locally (I also needed to show the aligned sequences) . Is there any program I can use to do the local pairwise alignment of multiple sequences?? I just need t ...
pairwise alignment reference written 6.5 years ago by biostar150 • updated 4.8 years ago by Darked894.2k
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Answer: A: Appropriate Outgroups For Paralog Families
... You can select any gene from Human or mammals that belongs to the same gene family. You cannot ignore outgroup for phylogenetic analysis unless you only want to do neighbor joining tree (which is not used to/preferred to examine evolutionary changes across the lineages) BTW, we need to know what kin ...
written 6.5 years ago by biostar150
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Comment: C: Sort Sequences In A Fasta File According To The Sequence List In Another Fasta/T
... Thanks Pavel! Thanks to everyone who contributed. ...
written 6.5 years ago by biostar150
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Comment: C: Bioperl Generating Error, Please Help To Configure Bioperl!!
... Thanks Guys!! The problem was that I did not install the cpanm module using sudo -s. It was not root execution, tha's why the error.... ...
written 6.5 years ago by biostar150
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Comment: C: Sort Sequences In A Fasta File According To The Sequence List In Another Fasta/T
... Sorry, the IDs are both alpha-numeric and I corrected that above. ...
written 6.5 years ago by biostar150
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8 follow
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Sort Sequences In A Fasta File According To The Sequence List In Another Fasta/Txt File
... Hi Guys, I have a fasta file with thousands of sequences and another text file for the sequence ids ( each id in a new line and they are the list of same sequences but in different order than the sequences in the fasta file). Could your guys please help me sort the sequences in fasta file according ...
fasta sequence written 6.5 years ago by biostar150 • updated 5.7 years ago by Biostar ♦♦ 20
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Bioperl Generating Error, Please Help To Configure Bioperl!!
... Hi I am a novice perl programmer. I just installed bioperl in my mac and when I tried to invoke some programs it generates this king of error. Could you guys please help me understand what is the problem here?? Thanks!! Mac:Desktop darwin$ perl bioperl.pl Use of uninitialized value $inFile i ...
bioperl written 6.5 years ago by biostar150
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Comment: A: How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frame
... Thanks guys! @Pavel, I think it allows me to submit same frame for multiple sequences, but how do I include multiple sequences with different frames all as one batch submission? Also, Is there a way to omit the sequences with stop codons in the frames for translation?? @Biolab, so the script you men ...
written 6.5 years ago by biostar150
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Comment: C: How Can I Sort Blast Output Based On E-Value?
... Thanks Mike, good to know that as well. ...
written 6.5 years ago by biostar150
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Comment: C: How Can I Sort Blast Output Based On E-Value?
... Thanks Pgibas! The awk command works as needed! ...
written 6.5 years ago by biostar150

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