User: rororo

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rororo0
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Posts by rororo

<prev • 12 results • page 1 of 2 • next >
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HMMER output parsing script
... I did an hmmscan of some proteins against the CAZy database using the `domtblout`option. Now I want to filter out overlapping domains, based on the e-value. I found a script on research gate: #!/usr/bin/env sh # Yanbin Yin # 07/21/2015 # hmmscan output parser # Usage: sh hmmsca ...
perl hmm parser written 6 weeks ago by rororo0
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Comment: C: Batch Download websites from php database
... Yes I know that site and just fetching the cluster number was my first guess, but when I save site, only a small file with the content "Error connecting to the database !" appears. Also happens when I click the link you posted. Thanks for your help! ...
written 7 weeks ago by rororo0
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Batch Download websites from php database
... I am working on nematodes and want to download ESTs from Mark Blaxter's website: http://www.nematodes.org/NeglectedGenomes/NEMATODA/Steinernema/index.html The programm that curates the database seems outdated, so I guess I need to download them manually. Is there a solution for automating this? e. ...
unix php written 7 weeks ago by rororo0 • updated 7 weeks ago by LLTommy1.2k
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EggNOG 4.5 database
... Can someone explain me why there are two eggNOG 4.5 databases for Bacteria? There is the precomputed HMM database for bactNOG and bact_50 available here: http://eggnogdb.embl.de/download/eggnog_4.5/hmmdb_levels/ ...
eggnog hmm written 5 months ago by rororo0 • updated 5 months ago by jhc2.5k
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Comment: C: local blast: makeblastdb: Abort trap 6
... I found out that formatdb is superseded by the makeblastdb command ...
written 7 months ago by rororo0
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Comment: C: local blast: makeblastdb: Abort trap 6
... next problem: formatdb command is not found... ...
written 7 months ago by rororo0
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Comment: C: local blast: makeblastdb: Abort trap 6
... yes it is unformatted text, also when I display invisible characters, the only invisible character is the new line feed. I did not try uppercase, because makeblastdb with lowercase letters has already worked ---edit--- I found out that I only get that Abort trap: 6 error when I add the flag -parse_ ...
written 7 months ago by rororo0
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Comment: C: local blast: makeblastdb: Abort trap 6
... I had an excel sheet with 3 columns: consecutive number, name of gene, sequence therefore I copied everything into a text editor and replaced all tabs with underscore, all slashes/colons with underscore etc and added a bigger than sign to the beginning, so this: >1.gene atgttgcaagagaaagt ...
written 7 months ago by rororo0 • updated 7 months ago by genomax39k
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Comment: A: local blast: makeblastdb: Abort trap 6
... makeblastdb -in Cat19_prot.fasta -parse_seqids -dbtype prot ...
written 7 months ago by rororo0
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local blast: makeblastdb: Abort trap 6
... I am running a standalone Blast 2.6.0 on my Mac OS 10.12.2 with 1.6 Ghz intel core i5 8 GB 1600 MHz DDR3. Everytime when I want to build a blast database with the makeblastdb command, I get the following error: Building a new DB, current time: 01/24/2017 09:13:26 New DB name: /Users/***/bin/blas ...
fasta makeblastdb blast written 7 months ago by rororo0

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