Forum: Bioinformatics
10-17-2019, 05:24 PM
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Replies: 1
Views: 4,356
Hi all,
has anybody tried to run psiblast...
Hi all,
has anybody tried to run psiblast with -phi_pattern option? I tried the command with the pattern file as follows:
ID xerD.
PA RX[VL]Q[LM][LM]GH
and I kept getting the following...
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Forum: Bioinformatics
08-22-2019, 03:12 PM
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Replies: 6
Views: 1,152
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Forum: Bioinformatics
08-22-2019, 02:40 PM
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Replies: 6
Views: 1,152
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Forum: Bioinformatics
08-22-2019, 02:25 PM
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Replies: 6
Views: 1,152
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Forum: Bioinformatics
08-22-2019, 12:58 PM
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Replies: 6
Views: 1,152
esearch stuck
Hi,
I am using esearch (part of the edirect tools) and it seems that it gets stuck without feedback. I am using version 12.0
Any suggestions?
Thank you all
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Forum: Bioinformatics
02-27-2019, 02:59 PM
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Replies: 0
Views: 707
segmentation fault clustal omega
Dear all,
I've been getting a "Segmentation fault: 11" with clustal omega. Any ideas/suggestions of how to fix this error. I've been using the program form over three years with no problems....
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Forum: Bioinformatics
01-15-2019, 07:13 AM
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Replies: 2
Views: 876
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Forum: Bioinformatics
01-09-2019, 03:10 PM
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Replies: 3
Views: 1,267
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Forum: Bioinformatics
01-09-2019, 10:54 AM
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Replies: 3
Views: 1,267
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Forum: Bioinformatics
10-23-2018, 08:14 AM
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Replies: 36
Views: 5,631
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Forum: Bioinformatics
06-28-2018, 06:53 AM
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Replies: 1
Views: 1,119
clustlO
Just a follow up on my question. It seems that different versions of clusterO give slightly different results. Just upgraded to 1.2.4 and 2 or 3 of my sequence pairs identity scores changed from...
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Forum: Bioinformatics
06-25-2018, 04:55 PM
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Replies: 1
Views: 1,119
Clustal Omega
Dear All,
Has anyone noticed that the standalone clustal omega reports slightly different percent identities than its web counterpart? It seems that the identity values from the standalone version...
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Forum: Bioinformatics
06-11-2018, 03:47 PM
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Replies: 9
Views: 3,479
Thank you Markiyan.
Yes it does take DDR3 ECC...
Thank you Markiyan.
Yes it does take DDR3 ECC RDIMM. Appreciate your suggestions. I thought SSD is not good for continuous heavy IO. Actually, I was planning on the portable 1TB USB drive. Glad...
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Forum: Bioinformatics
06-09-2018, 05:20 PM
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Replies: 9
Views: 3,479
I agree. NCBI released the youtube video...
I agree. NCBI released the youtube video explaining how it works. I was impressed with the taxonomy. I am using in house for tests.
I will upgrade the memory of my MacPro soon.
Thanks for your...
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Forum: Bioinformatics
06-08-2018, 03:14 PM
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Replies: 9
Views: 3,479
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Forum: Bioinformatics
06-08-2018, 02:49 PM
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Replies: 9
Views: 3,479
GenoMax. Here are the links:
For the...
GenoMax. Here are the links:
For the executables:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.8.0alpha/
For the new database the goes with it:...
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Forum: Bioinformatics
06-08-2018, 02:41 PM
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Replies: 9
Views: 3,479
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Forum: Bioinformatics
06-07-2018, 01:43 PM
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Replies: 9
Views: 3,479
Blast 2.8.0+
Hi all,
I have been getting the following error:
Error memory mapping:/Volumes/cbbc_expansion1/BLASTDB/nt.43.nnd openedFilesCount=251 threadID=0
BLAST Database error: Error pre-fetching sequence...
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Forum: General
12-08-2017, 08:58 AM
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Replies: 2
Views: 1,500
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Forum: General
12-08-2017, 08:11 AM
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Replies: 2
Views: 1,500
BBmap make error
Hi all,
I am trying to "make" bbmap and I am getting this error:
BandedAlignerJNI.c:1:10: fatal error: jni.h: No such file or directory
Any advice?
Thank you
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Forum: Bioinformatics
05-23-2017, 11:39 AM
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Replies: 0
Views: 964
Microarray data
Hi all,
I was wondering if anybody knows how to estimate number of transcripts (abundance) from microarray data (for examples using RMA values). Is there a way to do so?
Best
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Forum: Bioinformatics
09-28-2016, 03:41 PM
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Replies: 5
Views: 1,659
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Forum: Bioinformatics
09-27-2016, 10:30 AM
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Replies: 5
Views: 1,659
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Forum: Bioinformatics
09-27-2016, 10:12 AM
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Replies: 5
Views: 1,659
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Forum: Bioinformatics
10-17-2014, 11:28 AM
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Replies: 4
Views: 1,528
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