Database and Annotation Tribolium

BLAST Against Baylor Data - Tribolum castaneum
Baylor College of Medicine - Annotator Login for Tribolium Annotation
Tribolium FTP and Wiky Site
Genboree Tribolium Project
The KSU Bioinformatics - A Tribolium genome database
The University of Cologne - Regular Tribolium Blast

Blast

FlyBase BLAST
General BLAST

DNA Tools

Analyzing DNA sequence data
VecScreen Screen
DNA, RNA, proteins format

Gene Prediction and PCR Primer Design

Primer3
FGenesH
GENSCAN Web Server at MIT
HMMgene Prediction of vertebrate and C. elegans genes
Eukaryotic GeneMark
GrailEXP

Alignments

pairwise alignments
Align Genestream 2 Institut de Genetique Humain, France
BLAST 2 SEQUENCE - NCBI
Pairwise Sequence Alignment - Michigan Technological Univ.
SIM Alignment Tool - Protein Sequences (Expasy - Switzerland) mirror sites: Canada, China, Korea, Taiwan, USA
multiple alignments
ClustalW: Kyoto Univ. , EBI site, EMBnet site
multalin: multalin site
sam: Pasteur SAM site
multiple alignment visualization
boxshade server
ESPript 2.0 server

Database searching

blastn - NCBI's BLASTN
blastp - NCBI's BLASTP
blastx - NCBI's BLASTX
FASTA - Univ. of Virginia

Hydropathic Profile determination

Plot the Hydropathic Profile of a Protein Weizmann Institute of Science Genome and Bioinformatics

Modelling resources

DOCK
DSSP database
EBI MaxSprout
FLEXX
Model Evaluation site
Prosa II site
SCWRL
Swiss-Model

Motif and Profile searching

input is a single sequence
Blocks Searcher Fred Hutchinson Cancer Research Center, Seattle
FPScan PRINTS scan with a protein sequence
Frame-ProfileScan server short DNA sequence against protein database (ISREC)
PANAL Univ. of Minnesota
prositepatterns mirror sites: Canada, Korea, Taiwan, USA, Profilescan server prosite profiles (ISREC)
input is meme generated pattern
mast page
mast intro
input is a series of related sequences
meme page [results via email]
meme intro, pratt site Univ. of Bergen, Norway

NCBI resources

documentation
Accession number
BLAST substitution matrices
dbEST summary
Fasta Format description
Genbank sample record
GI number
High Throughput Genomic Sequences
LocusLink and ReqSeq development
Molecule type
Reference Sequences
Version number
servers
BLAST 2 SEQUENCE
blastn - NCBI's BLASTN
blastp - NCBI's BLASTP
blastx - NCBI's BLASTX
CD-Search
Entrez search
LocusLink search
OMIM search

Protein family and Domain searching

CD-Search - NCBI [Cn3D viewer needed to display structures] pfam sites: Sanger Centre, Washington Univ.
Prodom page
SMART page

Secondary Structure prediction

Chou-Fasman Secondary Structure Prediction
GOR Secondary Structure Prediction
NNPREDICT Protein Secondary Structure Prediction
PredictProtein server

Software

ClustalW EMBL molecular biology distribution site (pick platform)
GeneDoc download page
Treeview download site

Visualization software

Chime download
Chimera download
CN3D download
Mage download
Rasmol download
Rasmol 2.7.2.1 site
Protein Explorer download
Swiss-PDB Viewer download, mirror sites: Canada, China, Korea, Taiwan, USA
WebLab Viewer Lite download

Software documentation

Rasmol 2.6

Structural databases

Dali database
FSSP database
ModBase database
NDB database
PDB database

Translation [DNA to protein]

Translation Machine EBI
Translate Tool (Expasy - Switzerland), mirror sites: Canada, China, Korea, Taiwan, USA

Transmembrane prediction

DAS - Stockholm University
HMMTOP - Hungarian Academy of Sciences
MEMSAT2 - results via email - University College London
PHDhtm - results via email -Columbia University - PredictProtein
PRED - TMR - University of Athens, Greece
Sosui - Tokyo University of Agriculture and Technology, Japan
Split - University of Split, Croatia
TMAP single - Karolinska Institutet, Sweden
TMHMM - CBS: Denmark
TMpred - EMBnet-CH
TopPred 2 Pasteur Institute
TSEG - Daisuke Kihara, Doctoral Student, Institute for Chemical Research, Kyoto University, Japan

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