Alignment Visualization Tool
AltAVisT compares two alternative multiple alignments of
the same sequence familiy; regions where both alignments
coincide are highlighted.
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
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 is a novel alignment program based on
segment-to-segment comparison.It is especially suited to
detect local similarities among distantly related
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 is a tool for the prediction of cis-regulatory
elements, e.g. PRE/TREs in Drosophila melanogaster.
OMA Optimal Multiple
Optimal Multiple Sequence Alignment
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.
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
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
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
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.