Where To Get Downloadable Annotated Microbial Transcriptome Sequences?

Question

[Tianyang Li]

Hi,

I'm interested in downloading some microbial transcirptome sequences for analysis, but I'm not sure which files in NCBI RefSeq release microbial contain the transcript sequences.

Does anybody know where I can get annotated microbial transcript sequences (downloadable and in FASTA format)?

Thanks.

[Neilfws]

Do you mean predicted transcripts or experimentally-verified?

[Tianyang Li]

@neilfws I mean experimentally-verified transcripts. Do you have any suggestions?

[Tianyang Li]

@neilfws: I mean experimentally verified transcripts, do you have any suggestions?

Answer 1

[Marina Manrique]

So far I know the NCBI EST database, that gathers transcripts from GenBank http://www.ncbi.nlm.nih.gov/nucest/. You can get all the EST files from the FTP ftp://ftp.ncbi.nlm.nih.gov/genbank/, the files gbest* but AFAIK they are in gbk format and all the EST are mixed altogether (from different organisms) so you would have to parse it and get only the microbial ones and in FASTA format,

you can also try the 'Batch Entrez' tool http://www.ncbi.nlm.nih.gov/sites/batchentrez where you get all the sequences providing a list of GIs or accession numbers,

HTH

Marina

Answer 2

[Casey Bergman]

You could also try the UCSC Microbes table browser, e.g. http://microbes.ucsc.edu/cgi-bin/hgTables?org=Streptococcus+pneumoniae+R6+&db=strePneu_R6_uid57859

This solves the fasta download but does not solve whether RefSeq mRNA are predicted are experimentally verified.

[Khader Shameer]

Thanks Casey, very useful.