User: Ghoti

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Ghoti40
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9 months, 2 weeks ago
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Posts by Ghoti

<prev • 16 results • page 1 of 2 • next >
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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 3 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 $PATH and hope it prioritizes based on order while also changing the mafft file name slightly to better distinguish the two versions. I've been navigating to the appropriate directory and issuing an authoritative command (./mafft), whic ...
written 3 months ago by Ghoti40
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Comment: C: Installing new MAFFT version
... Wasn't sure if code formatting was appropriate for an error report. Thanks for correcting. ...
written 3 months ago by Ghoti40
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Installing new MAFFT version
... I'm trying to update my MAFFT version without overwriting the existing version (it's difficult for me to get root access). I've created a pseudo bin folder to contain the new MAFFT files, but I seem to be unable to specify priority of the new MAFFT location (defaults to /user/local/bin). When I do c ...
mafft written 3 months ago by Ghoti40 • updated 4 weeks ago by Biostar ♦♦ 20
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Answer: A: Mafft Output Distance Matrix
... Apologies for updating an old topic, but this page is one of the first results when searching Google for "MAFFT distout". I'd like to share some information on the distout feature that comes directly from Dr. Katoh, author of MAFFT: > The --distout flag is just for my personal use and there is n ...
written 3 months ago by Ghoti40
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Answer: A: Long terminal gaps in MAFFT alignment
... Contacted the creator of MAFFT (Dr. Katoh), who suggested using a lep value of -0.5. This solved my terminal gap problem by "penalizing long internal gaps more strongly than terminal gaps. As a result, a terminal gap (W-----$) is inserted instead of the internal gap (-----W$) while the W/W match is ...
written 3 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 3 months ago by Ghoti40
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Running HMMER via Python
... I'm trying to run a profile HMM via Python. I've found a Python 2 package (SimpleHMMER: https://pypi.python.org/pypi/SimpleHMMER/0.2.1) that runs HMMER3 and parses the output. However, the package is not able to create HMM profiles. My goal is to create HMM profiles from a continuously updated conse ...
profile hmm python hmmer hmm cli written 3 months ago by Ghoti40
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Comment: C: Any alignment programs that accept regular expressions within input sequences?
... I need to perform tens of thousands of pairwise alignments in a few hours. Thus far I've been using MAFFT localpair (computes with Smith-Waterman algorithm). In order to preserve computation time, I thought that a simple change to the scoring matrix would be sufficient. However, the required MAFFT v ...
written 4 months ago by Ghoti40
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Comment: C: Any alignment programs that accept regular expressions within input sequences?
... Thanks for the suggestion. Profile HMM is basically what I described, but after reading up on it, I worry it will be overly computationally demanding. Perhaps instead I'll adjust scoring matrices. MAFFT in particular allows for a user defined 248x248 matrix (in alpha testing) which could use unique ...
written 4 months ago by Ghoti40

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