Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation

Similar Threads
Thread Thread Starter Forum Replies Last Post
Capillary sequencer market. pmiguel Sanger/Dye Terminator 4 07-02-2011 08:49 PM
Capillary and NGS data from the same sample szilva Bioinformatics 0 05-03-2011 06:33 AM
PubMed: Perspectives of DNA microarray and next-generation DNA sequencing technologie Newsbot! Literature Watch 0 01-20-2009 06:01 AM
Helicos sequencing: Single-Molecule DNA Sequencing of a Viral Genome eldfors Literature Watch 1 04-04-2008 09:19 AM

Thread Tools
Old 12-01-2010, 11:18 AM   #1
Junior Member
Location: canada

Join Date: Nov 2010
Posts: 6
Question Capillary DNA sequencing

hello all,

So my question is: is there a particular type of library i need to construct if i am to use capillary sequencing?

This is a question for an HW of mine, but I want to emphasize that I DONT WANT you to give me the answer!

I would just like to be pointed in the right direction, in terms of the theory behind building the appropriate library

Thank you
splicemaster is offline   Reply With Quote
Old 12-01-2010, 01:57 PM   #2
Junior Member
Location: canada

Join Date: Nov 2010
Posts: 6
Default Edit

hello all,

So I came to the conclusion that I should use a combination of cosmid and BAC libraries, as was used in the pibmed article 16372010

my issue now is how to use the following equation:

Genome coverage = (total # of clones - # of non-contributing clones) X
average insert size/haploid genome size

according to the poisson distribution, the probability of obtaining one or more clones per locus is a function of library size

in my case, I need 8fold coverage which would be 99.97%

btw, the genome im working with is 20Mb

i knw that in terms of cloning capacity, cosmids can take about 40 kb

and BAC can take up to 300kb

but I cant seem to put it all together

Common seqanswer community! help a newbie out

thank you
splicemaster is offline   Reply With Quote
Old 12-02-2010, 08:19 AM   #3
Registered Vendor
Location: Madison, WI

Join Date: May 2010
Posts: 89

I'd actually recommend using fosmids, rather than BACs or cosmids, but the principle is the same.Here's how to do the calculation (for more details, download the PDF from the first link on this page.)

Determining the Approximate Number of Clones for a Complete Fosmid Library:

Using the following formula, determine the number of fosmid clones required to reasonably ensure that any given DNA sequence is contained within the library.
N = ln (1-P ) / ln (1-f )
Where P is the desired probability (expressed as a fraction); f is the proportion of the genome contained in a single clone; and N is the required number of fosmid clones.

For example, the number of clones required to ensure a 99% probability of a given DNA sequence of E. coli (genome = 4.7 Mb) being contained within a fosmid library composed of 40-kb inserts is:
N = ln (1 – 0.99) / ln (1 – [4 x 10^4 bases / 4.7 x 10^6 bases]) = –4.61 / –0.01 = 461 clones

Hope that helps.
epibio is offline   Reply With Quote
Old 12-02-2010, 08:30 AM   #4
Junior Member
Location: canada

Join Date: Nov 2010
Posts: 6

much appreciated, helps a lot!

your company's site is prefect

splicemaster is offline   Reply With Quote

capillary, library construction

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 06:41 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO