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Old 12-15-2011, 03:31 AM   #1
kentsis
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Location: Boston, MA

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Default Exon-exon junctions

We need to create a custom human mRNA expression database containing reshuffled exon-exon junctions.

Can anyone point to a data source where we can download human mRNA sequences and their exon-exon junctions, which we can reshuffle using perl or the like?
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Old 12-15-2011, 07:53 AM   #2
BAMseek
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You might try the refFlat.txt.gz file, available here

http://hgdownload.cse.ucsc.edu/golde...hg19/database/

(for me, the access time of this page is pretty slow).

A description of the file format can be found here

http://genome.csdb.cn/cgi-bin/hgTabl...aTable=refFlat

The same exon can be represented in several transcripts, so it would be good to do a sort | uniq on the list of exons. Also be aware that exons can overlap.

Justin
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Old 12-18-2011, 06:32 AM   #3
zee
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Try the Useq http://useq.sourceforge.net MakeTranscriptome tool.


Quote:
Takes a UCSC ref flat table of transcripts and generates two multi fasta files of
transcripts and splices (known and theoretical). All possible unique splice junctions
are created given the exons from each gene's transcripts. In some cases this is
computationally intractable and theoretical splices from these are not complete.
Read through occurs with small exons to the next up or downstream so keep the sequence
length radius to a minimum to reduce the number of junctions. Overlapping exons are
assumed to be mutually exclusive.
You can then align all your reads and then use the http://useq.sourceforge.net/cmdLnMen...criptomeParser SamTranscriptomeParser to convert these back to genomic coordinates.


We have a full protocol on how to do this http://www.novocraft.com/wiki/tiki-i...he+Spliceosome

Last edited by zee; 12-18-2011 at 06:35 AM.
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