family.caltech.edu

FamilyJewels: tools for comparative sequence analysis

Tools for Comparative Sequence Analysis. This is the home page for the FamilyJewels project at Caltech. Where we are developing tools for biologists to do comparisons of genomic DNA on the order of 10-100kb in length. New users should start with the introduction to doing comparative sequence analysis with FamilyRelations II. There are two example class. Available for people interested in using FRII for a genomics class. They were both developed for classes at Caltech. August 26th, 2005. Mar 24, 2005.

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FamilyJewels: tools for comparative sequence analysis | family.caltech.edu Reviews

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Tools for Comparative Sequence Analysis. This is the home page for the FamilyJewels project at Caltech. Where we are developing tools for biologists to do comparisons of genomic DNA on the order of 10-100kb in length. New users should start with the introduction to doing comparative sequence analysis with FamilyRelations II. There are two example class. Available for people interested in using FRII for a genomics class. They were both developed for classes at Caltech. August 26th, 2005. Mar 24, 2005.

<META> KEYWORDS

1 familyjewels

2 of this functionality

3 projects

4 announcements

5 methods paper

6 software update

7 software

8 familyrelations ii

9 aka frii

10 the paircomp toolkit

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familyjewels,of this functionality,projects,announcements,methods paper,software update,software,familyrelations ii,aka frii,the paircomp toolkit,related projects,seqcomp,familyrelations,additional information,software availability,publications,yuh et al

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FamilyJewels: tools for comparative sequence analysis | family.caltech.edu Reviews

https://family.caltech.edu

Tools for Comparative Sequence Analysis. This is the home page for the FamilyJewels project at Caltech. Where we are developing tools for biologists to do comparisons of genomic DNA on the order of 10-100kb in length. New users should start with the introduction to doing comparative sequence analysis with FamilyRelations II. There are two example class. Available for people interested in using FRII for a genomics class. They were both developed for classes at Caltech. August 26th, 2005. Mar 24, 2005.

INTERNAL PAGES

family.caltech.edu

1

Optional Bi188 Project: Comparative Sequence Analysis

http://family.caltech.edu/project

Two possible projects using FamilyRelations. Due date: Monday, April 19th. The goal of these projects is to gain some understanding of how genomic DNA in general, and regulatory DNA in specific, has diverged between closely related species (such as mouse, human, and rat) and between more distantly related species (such as mouse and chick). There is a tutorial. To help you learn how to use FamilyRelations and Cartwheel. And chick (Gallus gallus). And use the pair view and triple view in FRII to answer som...

2

November, 2004 changes to Cartwheel/FamilyRelationsII

http://family.caltech.edu/update-nov-2004.html

November, 2004 changes to Cartwheel/FamilyRelationsII. Here's a rough list of the most recent changes to Cartwheel and FamilyRelationsII. Note that you'll need to download the latest version of FRII. To continue using Cartwheel; your older versions will no longer work. Cartwheel can now run blastz. Alignments, thus mimicking some of the functionality of PipMaker. Respectively. Pairwise VISTA comparisons can also be uploaded to the server but cannot be directly executed. Many of these changes are pretty s...

3

FamilyRelations II: A Tutorial

http://family.caltech.edu/tutorial

FamilyRelations II: A Tutorial. Comparative Sequence Analysis Made Easy, take II). C Titus Brown, titus@caltech.edu. Davidson Laboratory of Embryonic Gene Expression. California Institute of Technology. Last revised April 2004. This is a tutorial for people who would like to use FamilyRelations II. To compare two or three genomic sequences. It will lead you through several steps:. Checking to make sure you can run FamilyRelations II [1]. Creating an analysis on the Cartwheel Web server [2]. In order to r...

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cartwheel.idyll.org

Cartwheel Bioinformatics Toolkit - Trac

http://cartwheel.idyll.org/wiki

The Cartwheel Bioinformatics Toolkit. See the Cartwheel user site. And the FamilyJewels user site. All of the Cartwheel and FamilyJewels source stuff has been moved from the two SourceForge sites ( http:/ sf.net/projects/cartwheel. And http:/ sf.net/projects/familyjewels/. Into a single Subversion repository. All of the "active" projects are now available under /trunk/. Contains the active development code for FamilyRelationsII. You can check out individual modules like this:. Developers can use ssh:.

mussa.caltech.edu

mussa

http://mussa.caltech.edu/mussa/wiki/WikiStart

Feature Requests / Bugs. We be plundering the High Sequence Seas For the hidden Treasures of Conservation". Mussa is a bioinformatics tool for finding and visualizing regions of conserved DNA by comparing across several species. It has been found that conserved regions are frequently enriched for regions that are functionally important. Thus Mussa is a tool to help discover previously unknown functional DNA elements. Mussa's core algorithm is an N-way version of. 2009Nov17 - Mussa Updates:. The Mac OS X ...

mussa.caltech.edu

mussa

http://mussa.caltech.edu/mussa/wiki

Feature Requests / Bugs. We be plundering the High Sequence Seas For the hidden Treasures of Conservation". Mussa is a bioinformatics tool for finding and visualizing regions of conserved DNA by comparing across several species. It has been found that conserved regions are frequently enriched for regions that are functionally important. Thus Mussa is a tool to help discover previously unknown functional DNA elements. Mussa's core algorithm is an N-way version of. 2009Nov17 - Mussa Updates:. The Mac OS X ...

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FamilyJewels: tools for comparative sequence analysis

Tools for Comparative Sequence Analysis. This is the home page for the FamilyJewels project at Caltech. Where we are developing tools for biologists to do comparisons of genomic DNA on the order of 10-100kb in length. New users should start with the introduction to doing comparative sequence analysis with FamilyRelations II. There are two example class. Available for people interested in using FRII for a genomics class. They were both developed for classes at Caltech. August 26th, 2005. Mar 24, 2005.

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