DNA sequencing. Software for High-throughput alignment.

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minna
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DNA sequencing. Software for High-throughput alignment.

Post by minna » Wed May 05, 2010 8:09 am

Hi all,

I'm, currently working on a project in which I have two 96 well plates full of plasmids.

I have purified the plasmid DNA and sequenced the insert on an ABI3730 for all 192 samples.

I now wish to verify that the sequences I got out of the instrument match my reference sequences, which are saved in an excel file.

Does anyone know of any software in which I would be able to upload either the trace files or the FASTA file that contains all the sequences from the instrument, as well as the reference sequences from my excel file and check them all automatically to see if they are the same? (Using NCBI's BLAST to check 192 sequences individually is not something I would like to do!)

many thanks
minna

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JackBean
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Post by JackBean » Wed May 05, 2010 10:36 am

you have sequences in Excel? Takovou prasárnu jsem ještě neviděl :roll:

What about multiple alignment e.g. by ClustalW?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

minna
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Re: DNA sequencing. Software for High-throughput alignment.

Post by minna » Wed May 05, 2010 11:37 am

yeah, the company who sold us the plasmids sent us the sequences of the inserts in an excel file.

I'll have a look at ClustalW.

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JackBean
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Post by JackBean » Thu May 06, 2010 8:22 pm

just put it into FASTA and look for Clustal or T-COFFEE ;)
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

minna
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Post by minna » Mon May 24, 2010 12:18 pm

neither clustal or t-coffee were really suitable (or maybe i just don't really know how to use them properly).

They basically looked for similarities between all 96 samples and all 96 reference sequences, i really just need to do a pairwise alignment for 96 samples and their corresponding reference sequence at the same time and get the results out in some kind of format where it states the percent similarity and overlap.

any other ideas anyone?

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JackBean
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Post by JackBean » Tue May 25, 2010 9:54 am

so, the sequences are not overlapping?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

foster033
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Re: DNA sequencing. Software for High-throughput alignment.

Post by foster033 » Thu May 27, 2010 9:21 pm

We use Sequencher(genecodes) for alignment and mutational analysis. It's not a free program, but I believe you can download a demo copy at their site that disables certain features, like copy and save. However if you just wanted to check the alignment it should work.

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canalon
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Post by canalon » Fri May 28, 2010 12:56 pm

You can also try Geneius (v5.0 I think now), you can try the full version for 4 weeks. Great customer service, and it will do what you want.
Patrick

Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)

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JackBean
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Post by JackBean » Fri Jun 04, 2010 7:22 am

just few days ago, I run across BioLign

http://www.mbio.ncsu.edu/BioEdit/bioedit.html
(approx. in middle of the page)
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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