Tools for the Molecular Biology

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
Restriction Enzyme Mapping	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
Prediction of Secondary Structure
Prediction of Secondary Structure	PredictProtein	PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec	COLUMBIA UNIVERSITY
Sequence Format	BOXSHADE	Pretty Printing and Shading of Multiple-Alignmen	ISREC
Sequence Format	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

Tools for the Molecular Biology - Quick Access Table