SeqWeb Program Overview

Comparison
Gap	Uses the algorithm of Needleman and Wunsch to find the alignment of two complete sequences. It maximizes the number matches and minimizes the number of gaps.
BestFit	Makes an optimal alignment of the best segment of similarity between two sequences. Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman
Compare	Compares two peptide or nucleic acid sequences and creates a graph that shows where the two sequences are similar.
FrameAlign	Creates an optimal alignment of the best segment of similarity (local alignment) between a protein sequence and the codons in the forward frames of a nucleotide sequence
PileUp	Creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments.
PlotSimilarity	Plots the running average of the similarity among the sequences in a multiple sequence alignment
Pretty	Create a multiple sequence alignment and calculate a consensus sequence
Database Searching
BLAST	Seaches for sequences similar to a query sequence. The query and the database searched can be either peptide or nucleic acid in any combination
NetBLAST	Seaches for sequences similar to a query sequence. The query and the database searched can be either peptide or nucleic acid in any combination
FastA	Performs a Pearson and Lipman search for similarity between your sequence and a database of sequences
SSearch	Searches a database using a rigorous Smith-Waterman Search for similarity between a query sequence and a group of sequences of the same type.
MotifSearch	Searches a database using a set of MEME profiles. You must first run MEME to create the profiles. You run MotifSearch from the MEME result page.
ProfileSearch	Searches a database using a profile created from unaligned sequences. The sequences are aligned and a position-specific scoring table is created. This table, called a profile, quantitatively represents the information in the alignment
LookUp	Identifies sequence database entries by name, accession number, author, organism, keyword, title, reference, feature, definition, length, or date.
StringSearch	Identifies sequences by searching for character patterns in the sequence documentation.
Evolutionary Analysis
GrowTree	These programs align a group of sequences, create a table of pairwise distances based on the aligned sequences, and create a tree graph representing the sequence relationships.
Mapping
Map	Displays your nucleic acid sequence with restriction enzyme cut points and protein translations. Or, displays a cleavage map of your peptide sequences.
Pattern Recognition
Frames	Displays open reading frames for the six translation frames of a DNA sequence.
MEME	Finds conserved motifs in a group of unaligned sequences.
Motifs	Looks for sequence motifs by searching through proteins for the patterns defined in the PROSITE Dictionary of Protein Sites and Patterns
ProfileScan	Uses a database of profiles to find structural and sequence motifs in a protein sequence
FindPatterns	Identifies sequences that contain short patterns. You can define the patterns ambiguously and allow mismatches
Primer Selection
Prime	Selects oligonucleotide primers for a template DNA sequence.
Protein Analysis
PeptideStructure	Makes secondary structure predictions for a peptide sequence
CoilScan	Locate coiled-coil segments in protein sequences.
HTHScan	Locate helix-turn-helix motifs in protein sequences.
SPScan	Locate secretory signal peptides in protein sequences.
PeptideSort	Shows the peptide fragments from a digest of an amino acid sequence
PepPlot	Plots predicted protein secondary structure and hydropathy plot
Moment	Makes a contour plot of the helical hydrophobic moment of a peptide sequence
HelicalWheels	Plots a peptide sequence as a helical wheel to help you recognize amphiphilic regions or beta sheets
Isoelectric	Plots the charge as a function of pH for a peptide sequence
RNA Secondary Structure
MFold	This program from Michael Zuker predicts optimal and suboptimal RNA secondary structures
StemLoop	Finds stems (inverted repeats) within a DNA or RNA sequence.
Translation
Translate	Use Translate to create a peptide sequence from an nucleic acid sequence
Reverse	Use Reverse to take to complement or the reverse your nucleic acid sequence
BackTranslate	Use BackTranslate to translate your peptide sequence into a nucleic acid sequence. Choose either the most probable nucleic acid sequence (utilizing a codon frequency table) or the most ambigious nucleic acid sequence