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Database Searching
H	BLAST	Search for similarities. [NCBI] or [WU]
H	Findpatterns	Search for short patterns in sequences. [basic] or [advanced]
H	Stringsearch.	Search for text patterns in sequence references with Stringsearch
Protein Analysis
H	Isoelectric	Analyze a protein sequence. [basic] or [advanced]
H	Moment	Analyze a protein sequence. [basic]
H	Motifs	Analyze a protein sequence. [basic] or [advanced]
H	Pepplot	Analyze a protein sequence. [basic] or [advanced]
H/H	Peptidestructure	Analyze a protein sequence. [basic] or [advanced]
H	Peptidesort	Analyze a protein sequence. [basic] or [advanced]
H	Coilscan	Analyze a protein sequence. [advanced]
H	Helicalwheel	Analyze a protein sequence. [advanced]
H	HTHscan	Analyze a protein sequence. [advanced]
H	SPScan	Analyze a protein sequence. [advanced]
DNA and RNA Analysis
H	Map	Analyze a DNA sequence. [basic] or [advanced]
H	Mapplot	Analyze a DNA sequence. [basic] or [advanced]
H	Translate	Analyze a DNA sequence. [basic]
H	Findpatterns TFD	Search a DNA sequence for transcription factors.
H	Fitconsensus	Search a DNA sequence for consensus patterns.
H	Testcode	Search a DNA sequence for potential protein coding regions.
H	MFOLD	Analyze an RNA sequence.
H	Stemloop	Analyze an RNA sequence.
Comparisons, Alignments & Trees
H	Bestfit	Bestfit pairwise alignments. [basic] or [advanced]
H	Gap	Gap pairwise alignments. [basic] or [advanced]
H/H	Compare	Compare two sequences and plot points of similarity using DotPlot. [basic] or [advanced]
H	FrameAlign	Align a protein sequence with codons derived from a DNA sequence.
H	Pileup	Create multiple sequence alignments with the Pileup program. There are three different versions of the program. Pileup for 10 pasted in sequences, Pileup2 using a list file and Pileup3 using a fasta collection file. Also see the ClustalW & Multalin pages.
H/H	Distances	Basic distance analysis and Growtree phylogenetic tree output.
H	Plotsimilarity	Plotsimilarity displays average similarity amoung sequences in a multiple sequence alignment.
H	Pretty	Pretty calculates a consensus sequence from a multiple sequence alignment file.
H	Prettybox	Prettybox displays a multiple sequence alignment in postscript form with shadings to show similarities.
Primer Analysis and Picking
H	MeltTemp	Checking designed primer melting point.
H	Prime	Select a primer. [basic] or [advanced]
H	PrimeLoop	Looping primer analysis.

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