User: Ghoti

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Ghoti40
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40
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2 months, 2 weeks ago
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1 year, 4 months ago
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B*************@ARS.USDA.gov

Posts by Ghoti

<prev • 19 results • page 1 of 2 • next >
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Standard for translating aligned nucleotide sequence
... I'm trying to derive translations from nucleotide alignments. I'm particularly concerned with insertions/deletions which change the reading frame. For insertions, I omit translating the added nucleotides. I'm looking for advice on deletion treatment. I can treat the frameshift as biologically releva ...
annotation alignment translation written 11 weeks ago by Ghoti40
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Comment: C: Annotation convention when dealing with sequencing error/ambiguity
... I'm trying to develop a predominantly automatic annotation tool. The biological interpretation of sequences can be influenced by a variety of factors. Factors which can be explored in more detail manually. I was hoping for a generic approach that could fit most/all sequences without special treatmen ...
written 4 months ago by Ghoti40
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Annotation convention when dealing with sequencing error/ambiguity
... I'm annotating sequences for use in a database. When dealing with a sequence that has obvious error at the terminal end/s, is it reasonable to salvage/annotate as much biological plausible information as possible, or does any sequencing error cast doubt on the reliability of the sequence as a whole? ...
sequencing written 4 months ago by Ghoti40 • updated 4 months ago by lieven.sterck3.3k
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Answer: A: Installing new MAFFT version
... A simple change to the Makefile fixed the problem, documented [here][1]. [1]: https://mafft.cbrc.jp/alignment/software/installation_without_root.html ...
written 9 months ago by Ghoti40
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Comment: C: Installing new MAFFT version
... Thanks for the suggestion. I'll try to prepend the directory to $PATH and hope it prioritizes based on order while also changing the mafft file name slightly to better distinguish the two versions. I've been navigating to the appropriate directory and issuing an authoritative command (./mafft), whic ...
written 10 months ago by Ghoti40
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Comment: C: Installing new MAFFT version
... Wasn't sure if code formatting was appropriate for an error report. Thanks for correcting. ...
written 10 months ago by Ghoti40
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Installing new MAFFT version
... I'm trying to update my MAFFT version without overwriting the existing version (it's difficult for me to get root access). I've created a pseudo bin folder to contain the new MAFFT files, but I seem to be unable to specify priority of the new MAFFT location (defaults to /user/local/bin). When I do c ...
mafft written 10 months ago by Ghoti40 • updated 7 months ago by Biostar ♦♦ 20
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Answer: A: Mafft Output Distance Matrix
... Apologies for updating an old topic, but this page is one of the first results when searching Google for "MAFFT distout". I'd like to share some information on the distout feature that comes directly from Dr. Katoh, author of MAFFT: > The --distout flag is just for my personal use and there is n ...
written 10 months ago by Ghoti40
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Answer: A: Long terminal gaps in MAFFT alignment
... Contacted the creator of MAFFT (Dr. Katoh), who suggested using a lep value of -0.5. This solved my terminal gap problem by "penalizing long internal gaps more strongly than terminal gaps. As a result, a terminal gap (W-----$) is inserted instead of the internal gap (-----W$) while the W/W match is ...
written 10 months ago by Ghoti40
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Comment: C: Running HMMER via Python
... Thanks for the quick response. Looks like that might do the trick. I'll give it a try. ...
written 10 months ago by Ghoti40

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Scholar 8 months ago, created an answer that has been accepted. For A: Installing new MAFFT version

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