User: fishgolden

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fishgolden390
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Posts by fishgolden

<prev • 92 results • page 1 of 10 • next >
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Comment: C: percent identities for all by all protein alignment
... > In Clustal Omega, the alignments are then computed using the very > accurate HHalign package (Söding, 2005), which aligns two profile > hidden Markov models (Eddy, 1998). http://msb.embopress.org/content/7/1/539 It seems that Clustal Omega uses HHalign. > A distance is calculated ...
written 5 weeks ago by fishgolden390
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Comment: C: percent identities for all by all protein alignment
... > but other threads on the site have shown that its pairwise alignments > can be a bit janky. Oh, really. I didn't know that. Thank you for the comment. ...
written 5 weeks ago by fishgolden390
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Comment: C: percent identities for all by all protein alignment
... CLUSTAL and MAFFT are Multiple Sequence Alignment software that they perform stringent DP (edit: jrj.healey said CLUSTAL's alignment is a bit janky Its alignment may not be stringent one...) same as water and needle when they are used as pairwise aligner. I mean, I think CLUSTAL and MAFFT are over s ...
written 5 weeks ago by fishgolden390
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Answer: A: percent identities for all by all protein alignment
... > There is some sort of filtering still going on, it would appear. > Hopefully I'm just missing some parameter? > > I'd hard code it myself but I'd rather have one of these algorithms do > it for me, as they'll presumably be faster at full scale. I think this is really difficult tas ...
written 5 weeks ago by fishgolden390
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Comment: C: Tool suggestions for bulk domain analyses?
... Oh, sorry. I thought you have id of transcripts or genes somehow because you could do DE analysis. BTW, Pfam website accepts multiple sequences with "search"->"batch search". ...
written 9 weeks ago by fishgolden390
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Answer: A: Tool suggestions for bulk domain analyses?
... How about DAVID ( https://david.ncifcrf.gov/ ) or TargetMine ( https://targetmine.mizuguchilab.org/ ) ? Both have domain enrichment analysis function(s). ...
written 10 weeks ago by fishgolden390
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Comment: C: (solved) I couldn't reproduce the problem of max_target_seqs
... I made several dummy dbs and ran searches several times but I couldn't reproduce the problem. There are many things to consider. - How long is the length of the query sequence? - Does it contain N? - How long is the lengths of -perc_identity 99 hits? - Are they masked? - How are the alignment ...
written 11 weeks ago by fishgolden390
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Comment: C: Install trimmomatic on windows computer?
... I could run trimmomatic with windows 10 Home + openjdk version "1.8.0_192" OpenJDK Runtime Environment (build 1.8.0_192-amazon-corretto-preview2-b12) OpenJDK 64-Bit Server VM (build 25.192-b12, mixed mode) ...
written 4 months ago by fishgolden390
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Answer: A: PSSM format for command-line PSIBLAST
... I think you have an ascii pssm file. I think psi-blast accepts only asn.1 format file as pssm which is non-human-friendly format. The asn.1 format files can be downloaded from cdd FTP site ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/ as cdd.tar.gz . BUUUUUT using that pssm, I got an error as follows (I t ...
written 4 months ago by fishgolden390
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Comment: C: Help with dynamic programming algorithm
... I see. Now I understand. That is >Because global alignment is the method which is designed to find optimal alignment utilizing all regions of both sequences. With that procedure, the gap length in 5' region becomes shorter & the alignment tends to utilize all regions. Please imagine two se ...
written 5 months ago by fishgolden390

Latest awards to fishgolden

Scholar 5 weeks ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Popular Question 3 months ago, created a question with more than 1,000 views. For (solved) I couldn't reproduce the problem of max_target_seqs
Supporter 5 months ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 7 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Student 7 months ago, asked a question with at least 3 up-votes. For (solved) I couldn't reproduce the problem of max_target_seqs
Autobiographer 20 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction

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