Software Tools :: Sequence Alignments and Comparisons
Background
Pairwise Sequence Alignments
Multiple Sequence Alignments
References
Programs
Pairwise alignments and comparisons
- GCG Programs
- Gap: Needleman-Wunsch global alignment
- BestFit: Smith-Waterman local alignment
- FrameAlign: Finds the optimal local alignment between a protein and a DNA sequence
- Compare: Finds regions of similarity between two sequences
using either a window/stringency or a word-based criterion (use
output as input to DotPlot)
- DotPlot: Creates a dotplot from the information found by Compare
- Overlap: Looks for overlaps between two DNA sequences using
the word-based Wilbur-Lipman algorithm
- EMBOSS Programs
- needle: Needleman-Wunsch global alignment
- water: Smith-Waterman local alignment
- matcher: Finds the best local alignments between two sequences
- stretcher: Finds the best global alignment between two sequences
- supermatcher: Finds a match of a large sequence against one or more sequences
- wordmatch: Finds all exact matches of a given size between 2 DNA sequences
- dotmatcher: Displays a thresholded dotplot of two sequences
- dottup: Displays a wordmatch dotplot of two sequences
- dotpath: Displays a non-overlapping wordmatch dotplot of two sequences.
- polydot: Displays all-against-all dotplots of a set of sequences
- est2genome: Aligns EST and genomic DNA sequences
- seqmatchall: Does an all-against-all comparison of a set of sequences
Multiple alignments
- GCG Programs
- Pileup: Creates a multiple alignment from a set of sequences
- HmmerAlign: Creates a multiple alignment from a large set of sequences using an HMM built by HmmerBuild from a small seed alignment
- Lineup: Manually edit a multiple sequence alignment
- SeqLab (X11-based): Manually edit a multiple sequence alignment in a color graphics environment
- Other Programs
- ClustalW: Creates a multiple alignment from a set of sequences
Related Tools
- GCG Programs
- Pretty: Displays a multiple sequence alignment; creates a consensus sequence
- PrettyBox: Displays aligned sequences in PostScript format, using shading to represent consensus regions
- NoOverlap: Finds regions where two or more DNA sequences have no subsequences in common
- PlotSimilarity: Plots the degree of similarity among sequences in a multiple sequence alignment
- GapShow: Displays an alignment (from Gap or BestFit) graphically, showing distribution of similarities and gaps
- EMBOSS Programs
- diffseq: Finds differences (SNPs) between nearly identical sequences
- cons: Creates a consensus from multiple alignments
- prettyplot: Displays aligned sequences, with coloring and boxing
- showalign: Displays a multiple sequence alignment
- infoalign: Privides information about a multiple sequence alignment
- plotcon: Plots the quality of conservation of a multiple sequence alignment
This website will look much better in a browser that supports
web standards, but it has been designed so
that it is still usable and accessible to any browser or web-enabled device.
|
