Alignments

• AltAVisT Alternative Alignment Visualization Tool

  AltAVisT compares two alternative multiple alignments of the same sequence familiy; regions where both alignments coincide are highlighted.

• ChromA Chromatogram Alignment

  ChromA provides the Dynamic Time Warping algorithm for the alignment of data from the domain of Gas- and Liquid-Chromatography Mass-Spectrometry. It uses additional constraints and can be configured to use different local functions to evaluate the similarity of mass spectra between chromatograms. It allows the definition of anchors, which are the positions of conserved compounds, constraining the alignment and providing a speedup. Furthermore, ChromA provides different visualizations of the alignment, as well as a textual format for further processing of chromatograms.

• DCA Divide-and-Conquer Multiple Sequence Alignment

  DCA is a very fast sequence alignment algorithm producing high quality alignments (close to the optimal alignment under the sum-of-pairs score).

• DIALIGN Multiple Sequence Alignments

  DIALIGN is a novel alignment program based on segment-to-segment comparison.It is especially suited to detect local similarities among distantly related sequences.

• e2g A web based tool for efficiently aligning genomic sequence to EST and cDNA data

  e2g is a web-based tool which aligns genomic sequence to cDNA and EST data sets. The server hosts huge EST databases of a few gigabases in size in indexed data structures. This allows users to rapidly (i) detect new genes, (ii) verify the exon-intron structure of predicted genes, and (iii) determine splice variants in the uploaded genomic region of interest. The Web interface provides a graphical overview of the results. Alignments can be visualized and matching sequences downloaded for further processing.

• JALI Jumping Alignments

  Jumping Alignments Jali is an alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Watherman algorithm.

• JPREdictor

  jPREdictor is a tool for the prediction of cis-regulatory elements, e.g. PRE/TREs in Drosophila melanogaster.

• OMA Optimal Multiple Sequence Alignment

  Optimal Multiple Sequence Alignment

• Passta Protein annotation by secondary-structure based alignment

  Passta annotates a protein query by secondary structure alignments. In contrast to traditional methods in sequence analysis, it allows rearrangements between the query and one or more of the target domains.

• PoSSuMsearch Fast and Sensitive Matching of Position Specific Scoring Matrices Using Enhanced Suffix Arrays

  Fast and Sensitive Matching of Position Specific Scoring Matrices Using Enhanced Suffix Arrays

• PoSSuMsearch2 Significant speedup of database searches with HMMs by search space reduction with PSSM family models

  Significant speedup of database searches with HMMs by search space reduction with PSSM family models

• SWIFT suit Fast Local Alignment Searching

  The SWIFT suit is a software collection for fast index-based sequence comparison. It contains the following programs: SWIFT — fast local alignment search, guaranteeing to find epsilon-matches between two sequences; SWIFT BALSAM — a very fast program to find semiglobal non-gapped alignments based on k-mer seeds.

• TSDA target site duplication align

  TSDA(target site duplication align) is an alignment tool to analyse recombinant DNA sequences. The program calculates (local) similarity of two sequences and shows the optimal alignment(s). The development was done using the algebraic dynamic programming (ADP) method.