Internet Resources

 
Bioinformatics & Genomics


 
Genomics & DNA Sequence Analysis



 
Comparative Genomics



 
DNA Sequence Analysis



 
DNA Sequencing Software



 
Genomic Search Servers



 
Human Genome

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BASS
[Whitehead Institute for Biomedical Research] A software program for tracking, extracting, and base calling DNA sequencing gels.


[more info][11238]

Chromas1.2
[Technelysium] This program displays and prints chromatogram files from ABI automated DNA sequencers and Staden SCF files, and it allows the user to manipulate the sequences.


[more info][11240]

DNATools
[Carlsberg Laboratory] Software for handling and analysis of nucleotide and protein sequences.
This downloadable package also has special functions for EST and SAGE handling and analysis.


[more info][11249]

FAKtory
[Arizona Research Laboratories] FAKtory is a software environment for supporting DNA sequencing
projects. FAKtory runs on machines configured with the UNIX operating
system. It is called FAKtory because it employs our FAKII Fragment
Assembly Kernel that is a C-library of routines
incorporating our best algorithms for solving the shotgun assembly
problem. FAKtory is highly configurable and can perform fragment
clipping, prescreening, and tagging functions, shotgun assembly with or
without constraints, and sequence finishing. An extensible input/output
mechanism permits FAKtory to be inserted into any informatics
environment.


[more info][11764]

GelReader
[NCSA] A color imaging and analysis tool that extracts information from digitized electrophoretic gel images, allowing manipulation of lanes and bands.



[more info][11252]

Getlanes
[Washington School of Medicine] Software developed to track lanes in four-color, flourescence-based, electrophoretic gel images for use in large scale sequencing projects.



[more info][11254]

Peakmatcher Download Site
[University of Minnesota] Peakmatcher is an Excel macro that automates the creation
of a binary (1/0) table from semi-automated
fluorescence-based AFLP. It can utilize text output from ABI
PRISM Genotyper software.

[more info][13768]

Phrap
[CodonCode Corp.] Phrap is a program for DNA sequence assembly. Some of Phrap’s feature include: fast assemblies, consensus quality estimates, and improved identification and handling of repeats.

[more info][11995]

Phred Phrap Consed System Home Page
[University of Washington] This set of widely used programs does the following. Phred reads DNA sequencer trace data, calls bases, and assigns quality
values to the bases. Phrap assembles shotgun DNA sequence data. Consed is graphical tool for editing Phrap assemblies. SWAT and CROSS_MATCH do sequence similarity searches.


[more info][13444]

Retrak v1.5
[Washington Univ. – St. Louis] A retracking and analysis environment for processing a large volume of gel samples.



[more info][11276]

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Stanford Genome Technology Center
[Stanford University] This site provides information about the center’s informatics projects and links to DNA sequencing projects, software, and tools.

[more info][12000]