Computational Biology Analysis Links

Sequence Analysis
Evolutionary Relationships
PHYLIP
TreeBase- find,view,DL phylogenetic trees and data
Sequence Utilities
BCM Search Launcher: Sequence Utilities	Boxshade pretty printing and shading of multiple alignment files 8-18-00
SeqLogos	SeqTransform (my applet for simple sequence manipulation.)

Multiple Sequence Alignment	Consensus from Multiple Alignments(aln/msf)
Blocks finds conserved areas in unaligned protein seqs	ORF Finder(visual)seldom works
ClustalDB alignment based on results of database search	RepeatMasker2
ClustalW

Other Useful Sequence Utility Websites
ABCC Sequence Analysis Pages	Brunel Bioinformatics Group
ExPASy	ISU W2H: WWW GCG interface

Sequence Features
MEME 3.0	META PredictProtein server
NetGene2	ProfileScan Server
PSORT: protein sorting prediction	SplicePredictor plant
TFSEARCH: search transcription factor binding sites (ver 1.3)	tRNA Compilation 2000: searchable tRNA DB
tRNAscan-SE: tRNA searches	WWW Promoter Scan
MEROPS protease database	Prolysis

Similarity Searches
Align - global best fit (2 sequences)	Blast 2.0
BLAST 2 Sequences returns local alignments	FASTA v.3
LAlign - returns multiple local alignments (2 sequences)

Structure Prediction
3D-PSSM: Prot. fold ID via 1D&3D seq profiles w/2° struct & solvation potential info	HMMtop: ~90% acc transmembrane domain prediction
LOOPP: Threading	MEMSAT: 92% acc Transmembrane prediction software
MultiCoil: A program for predicting two- and three-stranded coiled coils	PSIpred: Top Secondary structure prediction server(78-80% acc)
TMpred: transmembrane domain prediction

Please direct any comments, corrections, or suggestions to: Brooke D. Peterson-Burch Copyright © 1998-2002 Druthilspar Industries, BioI Inc. All rights reserved. Copyright © 1998-2002 Brooke D. Peterson-Burch. All rights reserved. Information in this document is subject to change without notice. Any other products and companies referred to herein are trademarks or registered trademarks of their respective companies or mark holders. Last Modified: