Oregon State University

Table of online analysis tools

Subject

Program

Summary

Server

Database Search

WAIS

KW [Key Words Search]

DISC

SFgate

KW

DDBJ

getentry

ID [ID Search]

DDBJ

PubMed

KW

NCBI

Entrez

KW, ID

NCBI

Homology Search

BLAST

BLASTN, BLASTP, BLASTX, TBLASTN

GenomeNET

FASTA

FASTA, TFASTA

GenomeNET

SSEARCH

Smith-Waterman algorithm

JST

Sequence Analysis

DNA to AA

Translation - The Protein Machine

EBI

PROSCAN

Predicts Promoter Regions (putative eukaryotic Pol II promoter sequences)

NIH

Signal Scan

Find and list homologies of signal sequences

NIH

SSPN

Splice Site Prediction by Neural Network

BDGP

Gene Feature

Prediction of Exon/Promoter/ORF etc.

BCM

ORF Finder

Graphical analysis tool which finds all ORFs

NCBI

TFSEARCH

Searching Transcription Factor Binding Sites

GenomeNET

MOTIF

Searching Protein Sequence Motifs

GenomeNET

BLOCK

Protein Motif Search

HFCRC

MEME

Multiple EM for Motif Elicitation

NBCR

ClustalW

Multiple Sequence Alignment

GenomeNET

pI/Mw

Computation of the Theoretical pI and Mw

ExPASy

Restriction Enzyme Mapping

TACG Restriction Mapping

Restriction Enzyme Mapping and Analysis

UMASS

WebCutter

Restriction Enzyme Mapping and Analysis

Max Heiman

PCR

Oligo

Primer Design for PCR

PITT

Primer3

Primer Design for PCR

MIT

Web Primer

Primer Design for PCR and Sequencing

SGD

Tm

Prediction of Tm

VGC

PredictProtein

PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec

COLUMBIA UNIVERSITY

Sequence Format

BOXSHADE

Pretty Printing and Shading of Multiple-Alignmen

ISREC

ReadSeq

Sequence Format Exchange

ISHIKAWA Jun

Others

Codon Usage

Codon Usage Tabulated from GenBank

DISC

MassSearch

Searching SwissProt or EMBL by protein mass after digestion

CBRG

PSORT

Analysis and Prediction of Protein Sorting Signals Coded in Amino Acid Sequence

Tokyo

PROTFAM

Protein Classification

MIPS

Adapted from Atsushi Isoai

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