User: Goldbear

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Goldbear130
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6 years, 2 months ago
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8 years, 7 months ago
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Posts by Goldbear

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Database Of Small Molecules/Chemicals Bacterial Toxicity
... Hi, I don't know if it's bad form or not to answer my own question, but for anyone else interested I found a useful database for this purpose @ AmicBase and @ toku-e http://www.manetec-52.de/apps/amicbase_drugs-online/base.nsf http://antibiotics.toku-e.com/antimicrobial_3988.html ...
written 7.5 years ago by Goldbear130
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Comment: C: Database Of Small Molecules/Chemicals Bacterial Toxicity
... Thanks! Yes, I guess what I meant by 'toxic' was at first approximation, growth inhibitory. Although I didn't find a lot of hits in CDD, I was able to find some interesting publications that I'll list below for anyone else interested. http://www.ncbi.nlm.nih.gov/pubmed/16981005 ...
written 7.6 years ago by Goldbear130
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Database Of Small Molecules/Chemicals Bacterial Toxicity
... Is there a database that contains information about which chemicals are toxic to E. coli? We're doing a chemical genetics project and in this particular instance would like to leave out chemicals that would inhibit growth or greatly perturb the cellular state of E. Coli. Basically, I will be parsi ...
database written 7.6 years ago by Goldbear130
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Comment: C: Word Wrapping Alignment With Javascript/Css?
... Amazing! thanks. Now to figure out how to colorize the gaps and mismatches. ...
written 8.3 years ago by Goldbear130
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Word Wrapping Alignment With Javascript/Css?
... Hi all, I'd like to display an alignment of two sequences in html format. I'd like to word wrap the text so that the width of the alignment auto adjusts with the window. Does anyone know how to do this? I'm guessing it might involve some css or js? Thanks ...
alignment written 8.3 years ago by Goldbear130 • updated 8.3 years ago by Pierre Lindenbaum124k
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Comment: C: Aligning Short Reads To Homologous Sequences?
... Thanks! This was exactly what I was looking for. ...
written 8.4 years ago by Goldbear130
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Comment: C: Aligning Short Reads To Homologous Sequences?
... Hi, my reads are about 90bp. unfortunately the divergence is pretty far. Our strategy may be to fully sequence one representative species from our clade and then use that as a reference for the other species. Thanks! ...
written 8.4 years ago by Goldbear130
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Aligning Short Reads To Homologous Sequences?
... I'm working on a de novo transcriptome project and the genome has not been sequenced for our plant. In general, trinity is working pretty well, but we are seeing some spurious fusion genes (N terminus of gene A fused to C terminus of gene B). For the questions we are asking, having the correct ful ...
short aligner transcriptome written 8.5 years ago by Goldbear130 • updated 6.1 years ago by rob234king580
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Webtool For Fetching Pmids From Blast?
... Hi, I was wondering if there is a web service that extracts all of the PMIDs that are in the results for a BLAST search? Example: I input the sequence for enchanced FLP and get a list of all the PMIDs associated with the genbank entries. I believe this is possible by parsing the XML, just wonderin ...
blast written 8.5 years ago by Goldbear130 • updated 8.5 years ago by Casey Bergman18k
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Answer: A: Is It Possible To Extract From Ncbi Nr Database Plant Protein Sequences.?
... Alternatively, plantgdb maintains a uniprot-curated list of plant protein sequences. It should be the UniProt_Protein.tar.bz2 file in ftp://ftp.plantgdb.org/download/FASTA/ This will extract out A LOT of sequence files that I wanted to join into one big file. I had to use xargs to get around the 'a ...
written 8.6 years ago by Goldbear130

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