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User: dssouzadan

gravatar for dssouzadan
dssouzadan • 30
Reputation:
30
Status:
New User
Location:
Brazil
Last seen:
5 years, 10 months ago
Joined:
6 years, 7 months ago
Email:
d*********@gmail.com

Posts by dssouzadan

<prev • 8 results • page 1 of 1 • next >
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Comment: C: ncbi-blast warning: Selenocysteine (U) at position ** replaced by X
... Thanks for your reply! ...
written 6.5 years ago by dssouzadan • 30
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ncbi-blast warning: Selenocysteine (U) at position ** replaced by X
... Hi all, I just want to know what does this warning message means. There's a way to suppress blast+ warings? The old blast has a flag -warnings as parameter, but the blast+ doesn't. ...
blast written 6.5 years ago by dssouzadan • 30 • updated 6.5 years ago by Neilfws ♦ 49k
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Comment: C: Blast Report: Expect(2) = number instead of Expect = number, what does it means?
... Thanks for the answer. Now it makes sense! ...
written 6.6 years ago by dssouzadan • 30
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Comment: C: Remove species from nr
... you can use the same database passing the following command: -negative_gilist <String> Restrict search of database to everything except the listed GIs * Incompatible with: gilist, seqidlist, remote, subject, subject_loc ...
written 6.6 years ago by dssouzadan • 30
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Blast Report: Expect(2) = number instead of Expect = number, what does it means?
... Hi all, in the sample below is shown two alignments with Expect and Expect(2) report: Score = 248 bits (129), Expect = 1e-63 Identities = 213/263 (80%), Gaps = 34/263 (12%) Strand = Plus / Plus Query: 161 atatcaccacgtcaaaggtgactccaactcca---ccactccattttgttcagataatgc 217 ||||||| ...
blast written 6.6 years ago by dssouzadan • 30 • updated 6.6 years ago by David W ♦ 4.8k
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Clustal Omega usage: Where is the score summary output?
... When I use the clustal omega I can't generate the score summary to evaluate the multiple alignment. Using the --help command I saw that I can generate only the following alignment outputs: --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fa ...
alignment clustal omega written 6.6 years ago by dssouzadan • 30
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Answer: A: Remove species from nr
... You can check the taxonomy ID of the organism that you're studying and after search this ID at NCBI. After that, look for the type of sequences you're looking for, nucleotide or protein and browse all sequences from organisms that have this taxonomy. Than download the entire GI list. Use the GI lis ...
written 6.7 years ago by dssouzadan • 30
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How to analyze the ProDom output? I have some results to support the analysis, but I don't have the answers.
... Hi all, I have some results retrieved from ProDom database and I need to analyze the output from 3 inputs to check if they share the same conserved domains, the results points to same description of 'ribonucleoprotein', then intuitively we can conclude that they share same domains, but I need to aut ...
prodom alignment algorithm blast domains written 6.7 years ago by dssouzadan • 30

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