Using SeqWeb

SeqWeb is a web based version of the popular Genetics Computer Group (GCG) package. This package was first developed to run in a "command line environment" (very user unfriendly) on Unix based machines. It has since been adapted to run through the web in a much more user friendly manner.

What does it do?

SeqWeb has computer programs that can run a lot of different analyses on your data (either DNA sequences or protein sequences). There are many programs that you can run, and the programs can be divided by category:

• Comparison Software
  • Gap: Aligns two sequences. It maximizes the number matches and minimizes the number of gaps. Use it to globally align two nucleic acid or peptide sequences sequences.
  • BestFit: Makes an optimal alignment of the best segment of similarity between two sequences. Use it to align two nucleic acid or peptide sequences.
  • 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. Use it to align several nucleic acid or peptide sequences.
  • 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 it to align several nucleic acid or peptide sequences and calculate a consensus.

• 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. You can run BLASTN, BLASTP, TBLASTN, and BLASTX searches locally.
  • 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. You can run BLASTN, BLASTP, TBLASTN, and BLASTX searches against NCBI data.
  • 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.

• Reference Searching
  • 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.

• Evolution
  • 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. 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
  • 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.

• Primer Selection
  • Prime: Selects oligonucleotide primers for a template DNA sequence. The primers may be useful for the polymerase chain reaction (PCR) or for DNA sequencing.

• Protein Analysis
  • 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.

• Nucleic Acid Secondary Structure
  • 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.

• Translation
  • Translate: Use Translate to create a peptide sequence from an nucleic acid sequence.
  • Reverse: Use Reverse to take the 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.

In the next part of the course we will use SeqWeb to generate a restriction map of a DNA sequence.