Sequence Analysis on the Web

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SACS provides web interfaces to a number of sequence analysis tools. Those tools that require a minimum of supporting resources to function are open to the general public. Others requiring more support are reserved for the use of SACS subscribers.

	Programs fall into these general areas
Database searching	BLAST
Alignments	pairwise and multiple alignment tools
EMBOSS	wEMBOSS interface to the entire EMBOSS package and locally generated interfaces to selected EMBOSS programs
genome tools	various tools for looking at genome data
phylogenetics tools	various PHYLIP tools for looking at phylogenetic data
transmembrane protein TMD predictors and display	HMMTOP, Memsat, TMHMM and TOPO2

Database searching

sacs

BLAST	This page allows the user to do regular BLAST searches.
	Search locally the NCBI BLASTable databases and Uniprot's Swissprot and Trembl.

Alignments

Pairwise alignments

needle	Uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length.	public
stretcher	Needleman-Wunsch rapid global alignment of two sequences.	public
lalign	Lalign non-overlapping local alignment of two sequences.	public
matcher	Waterman-Eggert local alignment of two sequences.	public
water	Uses the Smith-Waterman algorithm (modified for speed enhancments) to calculate the local alignment.	public

Multiple alignments

ClustalW	Output from the Multiple Sequence Alignment program ClustalW(v1.8) can be color coded with mview for easier reading.	public
MultAlin	MultAlin, a Multiple Sequence Alignment tool designed by Florence Corpet, offers several comparison tables and has a gif output file which can be color coded.	public
muscle	A program for creating multiple alignments of amino acid or nucleotide sequences by R.C. Edgar that is faster than Clustalw.	public
t_coffee	A multiple sequence alignment program with many options.	public

EMBOSS Programs

wEMBOSS
Interface
wEMBOSS is a web interface to the EMBOSS software package for biological sequence analysis. wEMBOSS started as a coordinated effort from Martin Sarachu of the Argentinian EMBnet Node and Marc Colet from the Belgian EMBnet node. sacs

remap
Display restriction enzyme binding sites in a nucleotide sequence. public

transeq
Translate nucleic acid sequences. public

genome tools

gene finding
A tool for finding the location of a gene on either the human or mouse genomes and then going on to see other genes in that neighborhood. public

gene environments
A tool for comparing the gene locations across a number of species. public

phylogenetics tools

drawtree
PHYLIP's drawtree program with preset font and postscript output. no changes to font, label, or tree orientation possible public

drawtree advanced
PHYLIP's drawtree program with user selectable values. changes to font, label, or tree orientation possible sacs

drawgram
PHYLIP's drawgram program with preset font and postscript output. no changes to font, label, type or gram orientation possible public

drawgram advanced
PHYLIP's drawgram program with user selectable values. changes to font, label, type or gram orientation possible sacs

Transmembrane Segment Prediction and display programs

HMMTOP	HMMTOP is a transmembrane prediction tool developed by G.E. Tusnady and I. Simon. TOPO2 displays the prediction.	public
Memsat	Memsat is a transmembrane prediction tool developed by David Jones. TOPO2 displays the prediction.	public
TMHMM	TMHMM is a transmembrane prediction tool developed by A. Krogh, B. Larsson, G. von Heijne, and E.L.L. Sonnhammer. TOPO2 displays the prediction.	public
TOPO2	Display the topology of a transmembrane protein.	public

Consulting | Training | Resources | Documentation | Links

wEMBOSS Interface	wEMBOSS is a web interface to the EMBOSS software package for biological sequence analysis. wEMBOSS started as a coordinated effort from Martin Sarachu of the Argentinian EMBnet Node and Marc Colet from the Belgian EMBnet node.	sacs
remap	Display restriction enzyme binding sites in a nucleotide sequence.	public
transeq	Translate nucleic acid sequences.	public

gene finding	A tool for finding the location of a gene on either the human or mouse genomes and then going on to see other genes in that neighborhood.	public
gene environments	A tool for comparing the gene locations across a number of species.	public

drawtree	PHYLIP's drawtree program with preset font and postscript output.	no changes to font, label, or tree orientation possible	public

drawtree advanced	PHYLIP's drawtree program with user selectable values.	changes to font, label, or tree orientation possible	sacs

drawgram	PHYLIP's drawgram program with preset font and postscript output.	no changes to font, label, type or gram orientation possible	public

drawgram advanced	PHYLIP's drawgram program with user selectable values.	changes to font, label, type or gram orientation possible	sacs

Programs fall into these general areas

BLAST

needle

stretcher

lalign

matcher

water

ClustalW

MultAlin

muscle

t_coffee

wEMBOSSInterface

remap

transeq

gene finding

gene environments

drawtree

drawtree advanced

drawgram

drawgram advanced

HMMTOP

Memsat

TMHMM

TOPO2

wEMBOSS
Interface