SeqWeb Version 1.2
For use with the Wisconsin Package Version 10.1
Use these programs to compare two or more sequences.
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.
Use your sequences to search peptide and nucleic acid databases.
BLAST
Searches for sequences similar to a query sequence. The query and the database searched can be either peptide or nucleic acid in any combination. Blast runs it's searches on the local server. Use NetBLAST to run your search on the NCBI server at NIH.
NetBLAST
Searches for sequences similar to a query sequence. The query and the database searched can be either peptide or nucleic acid in any combination. NetBLAST runs it's searches on the NCBI server at NIH.
FastA
Performs a Pearson and Lipman search for similarity between your sequence and a database of sequences of the same type (peptide or nucleic acid). For nucleic acid searches, FastA may be more sensitive than BLAST.
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 (nucleic acid or protein). This may be the most sensitive method available for similarity searches. Compared to BLAST and FastA, it is very slow.
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. Use ProfileSearch to find sequences that are distantly related to a group of sequences.
Use these programs to search the reference information of sequence databases.
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.
Investigate the evolutionary relationships within a group of sequences.
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.
Use these programs to display restriction maps or peptide cleavage maps of your sequence.
Map
Displays your nucleic acid sequence with restriction enzyme cut points and protein translations. Or, displays a cleavage map of your peptide sequences.
These programs help you recognize coding regions, terminators, repeats, and consensus patterns. Several programs help you analyze sequence composition.
Frames
Displays open reading frames for the six translation frames of a DNA sequence. Frames can superimpose the pattern of rare codon choices if you provide it with a codon frequency table.
MEME
Finds conserved motifs in a group of unaligned sequences. MEME saves these motifs as a set of profiles. You can search a database of sequences with these profiles using the MotifSearch program.
Motifs
Looks for sequence motifs by searching through proteins for the patterns defined in the PROSITE Dictionary of Protein Sites and Patterns. Motifs can display an abstract of the current literature on each of the motifs it finds.
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.
This program helps you select oligonucleotide primers for a template DNA sequence.
Prime
Selects oligonucleotide primers for a template DNA sequence. The primers may be useful for the polymerase chain reaction (PCR) or for DNA sequencing.
Use these programs to perform protein analysis tasks.
PeptideStructure
Makes secondary structure predictions for a peptide sequence. These predictions include (in addition to alpha, beta, coil, and turn) measures for antigenicity, flexibility, hydrophobicity, and surface probability. The predictions are displayed graphically.
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. It sorts the peptides by weight, position, and HPLC relative retention, and shows the composition of each peptide. It also prints a summary of the composition of the whole protein.
PepPlot
Plots predicted protein secondary structure and hydropathy plot.
Moment
Makes a contour plot of the helical hydrophobic moment of a peptide sequence.
HelicalWheel
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.
These programs predict secondary structure in nucleic acid sequences.
MFold
This program from Michael Zuker predicts optimal and suboptimal nucleic acid secondary structures. Use MFold to predict and display RNA or DNA secondary structures.
StemLoop
Finds stems (inverted repeats) within a DNA or RNA sequence. You specify the minimum stem length, minimum and maximum loop sizes, and the minimum number of bonds per stem.
Use these programs to translate nucleic acids into peptide sequences and peptides back into nucleic acids.
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.