User: gtrwst9

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gtrwst90
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Posts by gtrwst9

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reference peptide database (post-translational products)
... Many databases when referring to a peptide give UniProt IDs, but these are too general and can refer to many cleavage products of a single gene. Is there a database which gives IDs for single peptides and has all (or most) of them? They could even be restricted to be bioactive. This would be of grea ...
peptides database reference proteins written 10 weeks ago by gtrwst90
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Comment: C: Complete phylogenetic trees?
... Thanks both. Acually ITOL provides complete trees in newick, nexus and phyloxml format so, presumably, also the distances. But their example tree has only a few hundred nodes. ...
written 7 months ago by gtrwst90
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Complete phylogenetic trees?
... Hello, where can I get trees with distance information of whole classes or kingdoms like bacteria? Someone must have done this already for the known genomes. Please note, distances must be included, else it would just be a taxonomic tree. ...
phylogenetic tree of life taxonomy tree written 7 months ago by gtrwst90
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Fosmid contamination in C. elegans genome?
... In the C. elegans chromosome X (NC_003284.9) is a complete copy of the C. elegans fosmid H05L03 (FO081428.1) at positions 5898291-5912640. I understand fosmids are vectors used to build sequencing libraries, so is this a contamination? ...
genome written 12 months ago by gtrwst90 • updated 12 months ago by Ahill1.6k
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command-line tool to split genome FASTA into equal chunks?
... Say I have the file for accession LS483306.1 which is one big sequence starting with >LS483306.1 xyz AGCT... and want to have one file with N sequences of size X, looking like this (example X=2000): >LS483306.1:1-2000 xyz AGCT... >LS483306.1:2001-4000 xyz GCTA... ...
software fasta conversion written 13 months ago by gtrwst90 • updated 3 days ago by Biostar ♦♦ 20
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Answer: A: Problem in processing SRA file from NCBI
... `fastq-dump --split-3 SRR...` This does NOT redownload everything. ...
written 13 months ago by gtrwst90
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Answer: A: convert SRA file into forward and reverse fastq files
... `fastq-dump --split-3 SRR...` This does NOT redownload everything. ...
written 13 months ago by gtrwst90
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Comment: C: linux 'cat' command merge fasta files without headers
... Probably the dash was surrounded by spaces. If you have filenames with spaces enclose the name with single or double quotes like `cat "Escherichia coli - genome.fa"`. ...
written 13 months ago by gtrwst90
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Answer: A: Taxa lists from Human Microbiome Project?
... Found it. This page lists the datasets grouped according to body sites: https://www.hmpdacc.org/hmp/HMASM/ and on this page: https://www.hmpdacc.org/hmp/HMSCP/ you can then download the abundance tables. Unfortunately skin sites are only one, the retroauricular. So my problem remains, although the ...
written 13 months ago by gtrwst90
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Taxa lists from Human Microbiome Project?
... Has anyone attempted to generate a list of taxa (at spec. body site), even without abundancies? This should be possible with the WGS part of the data, as 16S is too error prone. I would be very interested in having a list of the skin, esp. of the back. But a complete (as in all sites) list would be ...
hmp metagenomic written 13 months ago by gtrwst90

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Scholar 7 months ago, created an answer that has been accepted. For A: Complete phylogenetic trees?

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