Hi everyone, Do you know where I can find best bacterial DNA sequences?
NCBI or MGDB,
and How to get all these reads?
Many thanks, Feng
NCBI or MGDB,
and How to get all these reads?
Many thanks, Feng
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For NCBI go to the genome section. From there it should be obvious how to download the reads. Or you could read the help documents if you need more help.
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Also check out CMR at JCVI: http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi
JGI Genome Projects: http://www.jgi.doe.gov/genome-projects/Comment
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I had downloaded the 85 bacterial files from genbank release 189
that was 19GB decompressed
created the fasta from it
~5 hours
sort by species, create sub-databases, make consensus/index sequences,
align, list sequances by changes only
publish the compressed aligned species-subdatabases !
18000 bacteria, 823012 entries, amino-acid sequences ~2GB
I must have a thread at flutrackers
most frequent:
46323, Escherichia coli
20346, Helicobacter pylori
15134, Bacillus
13565, Listeria monocytogenes
13486, Vibrio
13331, Pseudomonas
13249, bacterium
11046, Neisseria meningitidis
11033, Mycobacterium
09981, Streptomyces
08615, Streptococcus pneumoniae
07850, Bradyrhizobium
07747, Salmonella entericasu
07012, Staphylococcus aureus
06620, Borrelia burgdorferi
05808, Bacillus subtilis
05547, Vibrio cholerae
05139, Clostridium perfringens
04547, Bacillus cereus
04479, Pseudomonas aeruginosa
04475, Streptococcus mutans
04319, Burkholderia
04308, Ralstonia solanacearum
04065, Chlamydia trachomatis
03992, Streptococcus mitis
03873, Haemophilus influenzae
03452, Legionella pneumophila
03405, Klebsiella pneumoniae
03335, Rhizobium
03229, Streptococcus pyogenes
03009, Bacillus thuringiensis
02997, Campylobacter jejuni
02969, Pseudomonas syringae
02876, ArthrobacterLast edited by gsgs; 12-01-2012, 07:28 PM.Comment
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