SeqWeb Version 1.1
For use with the
Wisconsin Package Version 10
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.
Globally align two nucleic acid sequences.
Globally align two peptide sequences.
- 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.
Locally align two nucleic acid sequences.
Locally align two peptide sequences.
- Compare
- Compares two peptide or nucleic acid sequences and creates a graph that shows where the two sequences are similar.
Compare and graphically display two nucleic acid sequences.
Compare and graphically display two peptide sequences.
- 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.
Create an optimal alignment.
- PileUp
- Creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments.
Align several nucleic acid sequences.
Align several peptide sequences.
- PlotSimilarity
- Plots the running average of the similarity among the sequences in a multiple sequence alignment.
Plot similarities among several nucleic acid sequences.
Plot similarities among several peptide sequences.
- Pretty
- Create a multiple sequence alignment and calculate a consensus sequence.
Align several nucleic acid sequences and calculate a consensus.
Align several peptide sequences and calculate a consensus.
Use your sequences to search peptide and nucleic acid databases.
- 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.
Nucleotide query against a nucleotide database (BLASTN).
Peptide query against a peptide database (BLASTP).
Peptide query against a nucleotide database (TBLASTN).
Nucleotide query against a peptide database (BLASTX).
Nucleotide query against a database with translation of both to protein (TBLASTX).
- 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.
Nucleotide query against a nucleotide database (BLASTN).
Peptide query against a peptide database (BLASTP).
Peptide query against a nucleotide database (TBLASTN).
Nucleotide query against a peptide database (BLASTX).
Nucleotide query against a database with translation of both to protein (TBLASTX).
- 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.
Search a nucleic acid database.
Search a peptide database.
Search a peptide database using a nucleic acid query, ignoring frameshifts (FastX).
Search a nucleic acid database using a peptide query, ignoring frameshifts (TFastX).
Search a nucleic acid database using a peptide query (TFastA).
- 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.
Search a nucleic acid database.
Search a peptide database.
- 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.
Use MEME to create profiles from nucleic acid sequences.
Use MEME to create profiles from peptide sequences.
- 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.
Search a peptide database using a Profile constructed from unaligned peptide 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.
Search database reference information.
- StringSearch
- Identifies sequences by searching for character patterns in the sequence documentation.
Search for character patterns.
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.
Construct Phylogenetic Trees from Nucleic Acid Sequences.
Construct Phylogenetic Trees from Peptide Sequences.
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.
Display a restriction map of your nucleic acid sequence.
Display a cleavage map of your peptide sequence.
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.
Show open reading frames for the six translation frames of a DNA sequence.
- MEME
- Finds conserved motifs in a group of unaligned sequences. MEME
Look for conserved motifs in nucleic acid sequences.
Look for conserved motifs in peptide sequences.
- 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.
Look for sequence motifs.
- ProfileScan
- Uses a database of profiles to find structural and sequence motifs in a protein sequence.
Use profiles to look for sequence motifs.
- FindPatterns
- Identifies sequences that contain short patterns. You can define the patterns ambiguously and allow mismatches.
Identify database sequences that contain short patterns.
Identify nucleic acid sequences that contain short user defined patterns.
Identify protein sequences that contain short patterns.
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.
Select primers for a template DNA sequence.
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.
Make secondary structure predictions for a peptide sequence.
- CoilScan
- Locate coiled-coil segments in protein sequences.
Locate coiled-coil segments.
- HTHScan
- Locate helix-turn-helix motifs in protein sequences.
Locate helix-turn-helix motifs.
- SPScan
- Locate secretory signal peptides in protein sequences.
Locate secretory signal peptides.
- 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.
Show the peptide fragments.
- PepPlot
- Plots predicted protein secondary structure and hydropathy plot.
Plot measures of protein secondary structure and hydrophobicity.
- Moment
- Makes a contour plot of the helical hydrophobic moment of a peptide sequence.
Make a contour plot of the hydrophobic moment.
- HelicalWheel
- Plots a peptide sequence as a helical wheel to help you recognize amphiphilic regions or beta sheets.
Plot a helical wheel.
- Isoelectric
- Plots the charge as a function of pH for a peptide sequence.
Plot charge as a function of pH.
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.
Predict optimal and suboptimal secondary structures for a nucleic acid sequence.
- 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.
Find stems within a sequence.
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.
Translate nucleic acid sequences into peptide sequences.
- Reverse
- Use Reverse to take to complement or the reverse your nucleic acid sequence.
Reverse nucleic acid sequences.
- 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.
Translate peptide sequences into nucleic acid sequences.
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