Forum: Bioinformatics
10-30-2019, 09:38 AM
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Replies: 1
Views: 1,473
What do you want to do with the text snippet...
What do you want to do with the text snippet next?
Can you program? If so, I would suggest looking at Biopython, BioPerl or a similar library which has a GenBank parser. They would let you parse...
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Forum: Bioinformatics
09-02-2019, 02:41 AM
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Replies: 3
Views: 1,529
OK. That is the latest release, good.
How...
OK. That is the latest release, good.
How did you install BLAST 2.9.0 on Windows 64? Was it using ncbi-blast-2.9.0+-win64.exe or ncbi-blast-2.9.0+-x64-win64.tar.gz (which one) from the NCBI FTP...
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Forum: Bioinformatics
08-30-2019, 10:37 AM
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Replies: 3
Views: 1,529
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Forum: Bioinformatics
10-15-2018, 04:57 AM
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Replies: 39
Views: 13,493
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Forum: Bioinformatics
05-22-2018, 08:35 AM
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Replies: 1
Views: 2,537
Looks like this issue? ...
Looks like this issue?
https://github.com/mummer4/mummer/issues/9
(I just ran into this error with mummer v3.23 and "gnuplot 5.0 patchlevel 5")
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Forum: Bioinformatics
02-10-2017, 09:33 AM
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Replies: 7
Views: 6,261
Here's a BLAST RBH tool I wrote earlier in...
Here's a BLAST RBH tool I wrote earlier in Python, which does consider duplicates and gives warnings about them:
https://github.com/peterjc/galaxy_blast/blob/master/tools/blast_rbh/blast_rbh.py
...
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Forum: Bioinformatics
02-10-2017, 09:28 AM
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Replies: 1
Views: 1,987
You could try a reference guided assembly,...
You could try a reference guided assembly, perhaps using MIRA?
You might want to first try mapping all the reads against the reference (with relaxed mapping settings) in order to divide the reads...
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Forum: Bioinformatics
02-01-2017, 03:00 PM
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Replies: 3
Views: 2,307
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Forum: Bioinformatics
02-01-2017, 09:58 AM
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Replies: 3
Views: 2,307
This might be worth reading:
Punta and Ofran...
This might be worth reading:
Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction,
or How To Use Sequence and Structure Information To Predict Protein
Function. PLoS Comput...
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Forum: Bioinformatics
01-27-2017, 12:54 PM
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Replies: 19
Views: 10,839
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Forum: Bioinformatics
10-31-2016, 04:11 AM
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Replies: 8
Views: 5,290
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Forum: Bioinformatics
10-30-2016, 02:56 AM
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Replies: 8
Views: 5,290
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Forum: Bioinformatics
10-26-2016, 08:26 AM
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Replies: 4
Views: 1,173
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Forum: Bioinformatics
10-26-2016, 08:10 AM
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Replies: 1
Views: 1,202
This is a near duplicate of your other thread...
This is a near duplicate of your other thread where you have been given advice and help: http://seqanswers.com/forums/showthread.php?t=72083
The .nal file is a plain text file describing how to...
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Forum: Bioinformatics
10-26-2016, 08:05 AM
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Replies: 4
Views: 1,173
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Forum: Bioinformatics
10-26-2016, 07:55 AM
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Replies: 8
Views: 3,673
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Forum: Bioinformatics
10-19-2016, 09:17 AM
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Replies: 8
Views: 3,673
My guess is this line has an extra slash:
...
My guess is this line has an extra slash:
blastn -query HPV2-C2_E1.fasta -db MV1SDB_a/ -out testblastout.txt
Try:
blastn -query HPV2-C2_E1.fasta -db MV1SDB_a -out testblastout.txt
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Forum: Bioinformatics
09-30-2016, 09:28 AM
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Replies: 5
Views: 1,659
The NCBI BLAST website does a lot of parameter...
The NCBI BLAST website does a lot of parameter optimisation for you based things like query sequence length - the gap settings in particular are worth checking compared to the command line defaults.
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Forum: Bioinformatics
08-29-2016, 03:48 AM
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Replies: 14
Views: 9,766
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Forum: Bioinformatics
08-29-2016, 03:36 AM
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Replies: 14
Views: 9,766
Thanks for emailing the files. Hmm. Where did...
Thanks for emailing the files. Hmm. Where did this "GenBank" files come from? That would be useful for us to know (e.g. for other people using the same tool), but right now my suggestion for setting...
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Forum: Bioinformatics
08-29-2016, 03:17 AM
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Replies: 14
Views: 9,766
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Forum: Bioinformatics
08-29-2016, 02:52 AM
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Replies: 14
Views: 9,766
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Forum: Bioinformatics
08-29-2016, 02:40 AM
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Replies: 14
Views: 9,766
Normally the first line (the LOCUS line) of a...
Normally the first line (the LOCUS line) of a GenBank file says if the record is DNA or protein - and Biopython uses that information. If this failed I would expect this error on trying to save as...
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Forum: Bioinformatics
07-30-2016, 02:18 PM
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Replies: 2
Views: 3,401
Very few mappers have support for circular...
Very few mappers have support for circular genomes (e.g. CLC mapper), and worse, the SAM/BAM format does not handle this well. As suggested by Tristan, mapping to a doubled linear reference can be a...
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Forum: General
04-10-2016, 11:34 AM
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Replies: 2
Views: 1,749
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