Bioinformatics Sequence Analysis


**The developer should have experience in Bio-informatics**

**Project Overview**:

Take raw DNA sequence data, (which will not be perfect), and compare it against the C. *elegans* genome, identify any location for a possible deletion, from those results, identify the most probable deletion site(s) and output the flanking left and flanking right sequence, insertion and/or ambiguous sequence if any.

The flanking sequence must be unique within the genome; typically, we have used 30 base pairs, but we have had to use more to make the sequence unique.

The program must handle several cases when determining deletion sites:

1. Insertions

2. Ambiguous sequence at the breakpoint site

3. More than one perfect match in the genome for the sequence. (Choose the Cosmid with the most hits to be the target region)

4. More than one perfect match of the same sequence occurred in the same Cosmid (Output both results to allow manual decision)

You can change the sequence below to produce the insertion or ambiguous breakpoints if you need too, as well as, test for perfect matches.

**(See attachment for sample sequence)**

I currently have looked into using Blast to tackle this issue and then parse the results. If there is another way that is as effective then please pursue it.

I can provide more information to get the project going and also if there are any questions, please contact me.

## Deliverables

- Perl script(s) that returns the flanking deletion sequences

-All associated 3rd party Perl modules and /or applications

- All deliverables will be considered "work made for hire" under U.S. Copyright law. Buyer will receive exclusive and complete copyrights to all work purchased.

* * *This broadcast message was sent to all bidders on Monday Nov 7, 2005 4:40:20 PM:

I will be choosing a bidder this week. I will be posting today some additional information to clarify this project.

I will email everyone when I have posted the new information.

Thank you for your time and patience.


* * *This broadcast message was sent to all bidders on Tuesday Nov 8, 2005 12:01:35 PM:

Please redownload the zip file for this project and read the pdf named Deletion Strategy, and provide me with your comments.



* * *This broadcast message was sent to all bidders on Tuesday Nov 15, 2005 12:10:07 PM:

I want to thank all the bidders for their input on this project. Most projects do not take this long to choose a bidder, but since this project involves several areas of expertise, it has taken longer to choose a bidder. I have choosen Evgeny Cheremushkin's bid and am currently having my company go through the bid acceptance process.

Good Luck to all you programmers on your projects. You all are an important resource to the community!



## Platform


OS: Linux

Programming Language: Perl

Habilidades: Engenharia, Linux, MySQL, Perl, PHP, Arquitetura de software, Teste de Software

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ID do Projeto: #3059380

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