vector end sequences (?)

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cjones
Posts: 99
Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
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vector end sequences (?)

Post by cjones » Thu Mar 01, 2007 8:28 pm

I think I've confirmed the vector sequences flanking the fosmid inserts:

...AGGTCGACTCTAGAGGATCCC [insert] GGATCCCCGGGTACCGAGCTCGAAT...

consed identified them as vector, and some of my students have seen these sequences at one or the other end of their projects. (Oddly, several have their projects in single contigs, but none of them have yet seen vector sequence at both ends of their contigs.)

This may be helpful for students trying to figure out which contigs are at the ends of the fosmid and their orientation, if consed doesn't snag it.
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

mshaw
Posts: 11
Joined: Sun Feb 04, 2007 10:26 pm

vector sequences

Post by mshaw » Tue Mar 27, 2007 4:53 pm

This didn't find anything for us. How about for others?
Mary Shaw

cshaffer
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Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
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vector sequence and finding the ends

Post by cshaffer » Tue Mar 27, 2007 5:31 pm

you will only find this sequence if you order a primer near the end of the insert that sequences back toward the vector. For all the reads that we rely on the sequences were generated from primers right next to the vector/insert boundary. This maximized the amount of mojavensis data from each read but does mean there is little to no vector sequence in the reads that would help find/orient the insert with the fosmid vectors.

You can find the reads that came from fosmid you are working with.
There is a post in this forum called "Two Big Contigs, and No Hints"

At the end is a list of all the projects and the names of the reads that correspond to the fosmid end reads.

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