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SeqAnalysis
Software

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.

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