This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Where To Get Downloadable Annotated Microbial Transcriptome Sequences?

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.

refseq transcriptome sequence
• 3,650 views • link
updated by Biostar Biostar • written by Tianyang Li • Tianyang Li

Do you mean predicted transcripts or experimentally-verified?

• 0 views • link
written by Neilfws Neilfws

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

• 0 views • link
written by Tianyang Li • Tianyang Li

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

• 0 views • link
written by Tianyang Li • Tianyang Li

2 answers

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

• 0 views • link
written by Marina Manrique Marina Manrique

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.

• 1 views • link
updated by Ram Ram • written by Casey Bergman Casey Bergman

Log in to answer this question.

More posts like this