K a m y a r F a r a h i with the 541 mates!
my email: kfarahi@verizon.net
dissertation title: Determining the evolution of the aminoacyl-tRNA synthetases
by the Ratios of Evolutionary Distances (RED) method
my guru: William B. Whitman
department: Department of Microbiology /directory/
school: University of Georgia /network status/ Red&Black
committee members: Eileen Kraemer, John McDonald, Rob Maier and Juergen Wiegel
collaborators: Ross Overbeek and Gordon Pusch
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Download RED-T application, which uses RED method to determine the evolution of the aminoacyl-tRNA synthetases
[my project's keywords: bioinformatics, genomics, phylogenetic analysis, phylogenomics, lateral gene transfer (LGT), tRNA-synthetase, ribosomal proteins, gene trees, evolutionary distance] |
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development and other technical resources:
bioinformatics.org - worthy of becoming your home page!
JAVA
Earthweb.com (used to be called GameLan) - great source for scripts of all sorts.
Javascript.com - our little Javascripts is growning up! Not bad to get some actions done quickly
Wrox - good reference site for developers
Perl: bioperl.org
UGA's SiteSoft - students can download software here
hardware: Tom's hardware guide
downloads: Download.com
NCBI: Blast, Sequin are some of the few
Phylip: phylogenetic analysis programs created by Joe Felsenstein
list of more phylogeny programs
Molphy: phylogenetic analysis programs (JTT matrix) created by J. Adachi, M. Hasegawa
GeneDoc: GUI for multiple sequence alignment data analysis created by K. Nicholas
ClustalX FTP: download this baby! Very user friendly GUI to generates multiple sequence alignments using various matrices (PAM, Gonnet, BLOSUM, etc.) , and also generate phylogenetic trees (limited to neighbor joining method). created by J. Thompson, T. Gibson, D. Higgins, F. Jeanmougin
[download directions for Windows: download the latest compressed version of the *.zip file (e.g. clustalx1.81.msw.zip)]
[operation notes: sequence files for analysis are best opened if in *.txt format]
tree drawing programs:
TreeExplorer - my favorite! Does everything you want, except analysis of boostrap values. I recommend importing a Newick standard file if you have created one. This is a supplement program of MEGA.
NJplot (this tool is also included in the ClustalX package) - good for viewing boostrap values if available. Also recognizes Newick standard file.
AVT - a phylogenetic tree display tool. This is a more powerful one than the above two. Editing is very easy and it is a JAVA app. You can access the applets also.
MEGA - Molecular Evolutionary Genetics Analysis software.
sample data can be found in these chapters of Molecular Evolution and Phylogenetics by authors, M. Nei and S. Kumar.
SeqAnal - sequence analysis... this is not bad!
LIBSHUFF - to compare clone libraries of sequence information and determine if they are significantly different created by David Singleton
Pedro's biomolecular research tools
Genome Net - Kyoto University's web-based bioinformatics tools
Sanger Center - list of sequencing software
WIT (aka ERGO) - created by Integrated Genomics and Argonne National Laboratory (license to access this database is required)
KEGG - Kyoto Encyclopedia of Genes and Genomes. Nice pathway interactive illustrations.
Milton Saier's Transport Links site at UCSD - find latest in transport research (e.g. COG's)
Web of Science: please log-off when you are done!
PubMed - NCBI site
MathSciNet - mathematical reviews on the web
ISCB - The International Society for Computational Biology
ISMB 2002 - International Conference on Intelligent Systems for Molecular Biology [August 3-7 at Edmonton, CANADA]
PSB - Pacific Symposium on Biocomputing [PSB Online Proceedings for 1996 - ]
PSB 2003 - January 3-7, 2003 at Kaua'i, USA
BOSC - Bioinformatics Open Source Conference
ASM - American Society for Microbiology
Download the poster presented at ASM 2001 - (compressed as a zip file)
GRC - Gordon Research Conferences
ISE - International Society of Extremophiles
Download the presented poster at the Naples, ITALY conference 2002 - (compressed as a zip file)
illustrations:
molecular art/science - created by David S. Goodsell
AE at national health museum - graphics gallery
school resources:
evolutionary biology links - Harvard University's Dept. of Molecular/Cellular Biology
The Phylogeny of Life - UCMP Phylogeny Wing at Berkeley
matrix background - not a bad overview of matrices available
Why Gonnet? read this!
Kosan Biosciences - leaders in research and development of novel polyketides
Wikipedia - The Free Encyclopedia
Erdos number project - what is it? and how can you computer your own Erdos number?
space photos: this is cool!
glossary of biological terms
31st surprise birthday party at The Globe, Athens. This is a link to my friend Hanz' site where he has kindly posted some pictures from the party. Thanks to my lovely wife, family and friends for making it a special night!
My photo album... - not much time to update this album, but I will soon!
Devan and Ethan Patel - to see the pictures of these cute guys, click here and then click on the 'pictures' link on the left navigation bar.
Iran - here is some lovely pictures of a lovely country. [by the way, it is pronounced 'ee-ron', NOT 'eye-ran'!]
The Day Our World Changed - children's art of 9/11.
Features:
Savor My Flavor - this is my brother's web site...
Careers:
Shopping:
edu.com - Not the most extensive tech selection, but you can't beat the prices! (need to be a registered student)
cnet.com - research the latest technology, and read professional and user reviews
Epionions.com - read reviews on anything you can think of... (broadway shows, stores...)
DealProvider.com - check out these coupons before shopping online.
Currentcodes.com - like DealProvider
Naughtycodes.com - also like DealProvider
TechDeals.net - same as the dealprovider site, but only for tech items
Digital Photography Review - source for most detailed reviews of cameras and equipment
ShutterFly.com - great site for uploading and developing prints for digital images
Movies:
IMDB.com - the greatest database of movies, actors, and anything about the film industry
QT - view the latest movie trailers
Travel:
Planet Edu - PlanetEdu is the fastest and most powerful search directory for international education
Study Abroad - if you got time, great... if you don't make time and do this!
Lonely Planet - great source for travelers
STA Travel - student friendly travel agency/site
Miscellaneous:
FLASH games - take a break and check out these games... you have to play eggfighter!
99X's Eric the Web Gangsta - tons of cool and useful web sites
Calories calculator - how much do you think you are burning per activity? find out...
Digital Blasphemy 3D - cool digital artwork... great for wallpapers
TestSpin.com - Earn money for surveys and get amazon.com gift certificates free (up to $600 per year)
Please submit any comments or suggestions to kfarahi@verizon.net
This site was created in the course of academic and research endeavors at the University of Georgia and not intended for any commercial use.
