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-   -   Which E. coli genome should I use (http://seqanswers.com/forums/showthread.php?t=61381)

arkilis 07-20-2015 09:16 PM

Which E. coli genome should I use
 
Hi guys,

There are a couple of genome sequence (rearrangement?) for E. Coli on the NCBI FTP. i.e.

Escherichia_coli_0127_H6_E2348_69_uid32571/
Escherichia_coli_042_uid40647/
Escherichia_coli_536_uid16235/
Escherichia_coli_55989_uid33413/

Now I am doing a (E. Coli) sequence alignment, which reference should I choose? Only know it is E. Coli.

thanks so much for your help.

GenoMax 07-21-2015 01:09 AM

Classic E. coli reference strain is E. coli K-12 strain MG1655 sequenced for the first time by Blattner et al in 1997. That strain is available here: http://www.ncbi.nlm.nih.gov/nuccore/U00096.3 (this may be equivalent to: ftp://ftp.ncbi.nih.gov/genomes/Bacte...1655_uid57779/)

That said you should ask the person you are working with as to what strain you should use for the analysis.

arkilis 07-21-2015 03:57 PM

Quote:

Originally Posted by GenoMax (Post 177775)
Classic E. coli reference strain is E. coli K-12 strain MG1655 sequenced for the first time by Blattner et al in 1997. That strain is available here: http://www.ncbi.nlm.nih.gov/nuccore/U00096.3 (this may be equivalent to: ftp://ftp.ncbi.nih.gov/genomes/Bacte...1655_uid57779/)

That said you should ask the person you are working with as to what strain you should use for the analysis.

Thank you GenoMax, so there is no generic one for alignment. I cannot find the person who submit the sequence, he left without a doc. So I was thinking to download all of them and align them one by one. Not quite sure I am doing the right thing?

Cheers,
Ben

Brian Bushnell 07-21-2015 04:13 PM

Aligning to all of them and picking the one with the highest alignment rate and the lowest error rate seems like the best solution, if you absolutely can't ask what the strain is.

GenoMax 07-21-2015 04:23 PM

@arkilis: What are you trying to do? Plain alignments/SNP calls post alignment/genome re-arrangements? Strains can differ significantly and choice you make may have an impact on your results. BTW: One I linked above is the classic lab strain people have used for years.

arkilis 07-21-2015 05:36 PM

Quote:

Originally Posted by GenoMax (Post 177836)
@arkilis: What are you trying to do? Plain alignments/SNP calls post alignment/genome re-arrangements? Strains can differ significantly and choice you make may have an impact on your results. BTW: One I linked above is the classic lab strain people have used for years.

Clear the data of a teammate who suddenly left. The folder name is E.coli. There are some sequences over there.:rolleyes:

Thank you.

SNPsaurus 07-21-2015 09:00 PM

I would blast 100 reads and check the results for the types that most often show a perfect match, then grab those references and align for a full analysis.


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