Search Results for "multiple sequence alignment" - Page 9

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. Annotates the locations of conserved elements in multiple sequence while correcting for alignment uncertainty and error.

CANGS DB is a user-friendly and stand-alone database tool for processing, analyzing and managing the high throughput sequencing data from 454 amplicon resequencing projects. CANGSDB is very easy to use; it could be installed and used on any UNIX based computer to handle individual as well as multiple sequencing projects. It provides full-fledged flexibility with various options in raw sequence processing and analysis. CANGS DB provides a very powerful data retrieval interface, which enables researchers to retrieve sample information and primers and barcodes information from any individual data set or from a combination of data set. ...

Image and video acquisition for scientific applications, particularly in behavioral biology and neuroscience

Multi-functional batch sequence aligner incorporating Needleman-Wunsch, Smith-Waterman and Oommen-Kashyap algorithms along with compound alignment of secondary sequences.

It's a browser based video editing tool that exports in FCP XML format. Give clients access to previews, mark in and out points and leaving comments, all in a sequence you can import directly into your project. Additional export formats coming soon.

ZAE is a Zoomable multiple sequence Alignment Editor

Autorun menu cum multi-purpose customizable utility menu / launcher for support personnel. Also happens to be a drop-in replacement for AMenu.

This is a utility to convert a set of fasta formatted sequences along with output from ELAND or SOAP (and other next generation sequence alignment in due time) to make them viewable using eagleview.

An efficient implementation of the Smith-Waterman algorithm that takes advantage of SIMD instruction sets in modern CPUs. The Smith-Waterman algorithm is used for sequence alignment in bioinformatics.

Mad Math is a Math API for Java that is aimed at adding needed math functions and formulas that are not in the regular Java Math API, such as fibonacci sequence, is prime, area formulas, greatest common factor, least common multiple etc.

AlViz is a research prototype for visual ontology alignment implemented as multiple-view plug-in for Protege using J-Trees and Graphs. Based on similarity measures of an ontology matching algorithm AlViz helps to assess and optimize the alignment results

This is a Perl module for doing snp analysis based on shotgun sequencing reads and a reference genome sequence. Its primary input is the cigar alignment format outputted from ssaha2.

BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.

PepT-IDE is a protein analysis tool that is used for multiple sequence alignment, 3D visualization and displaying protein contact maps for protein sequences and structures. It also has feedback communication between the different views of the protein.

SISSIz is a program for randomizing multiple sequence alignments preserving dinucleotide content. It can be used as a control strategy for comparative noncoding RNA gene prediction programs and as a standalone RNA gene finder.

J3dPSV 1.0 is a graphical application package for viewing and modeling of three dimensional structures of protein structure, including multiple chain sequence table and a three-dimensional (3D) protein structure viewer.

A tool to compare two Protein Sequences and show similarities with the help of dotplot.

Spectre for mass spectrometry. (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data. (working on mzDATA). Provides filters, alignment- and export tools.

Scripts to implement Hierarchical Annotation-Dependent Alignment (HADA) protocol for sequence alignment, and related functions.

POA is Partial Order Alignment, a fast program for multiple sequence alignment in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment.

Biological Annotation Tool is a general-purpose high speed environment for manipulating biological sequence annotations in multiple input and output formats. A plugin-style API permits much extensibility.

JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.

The set of tools for biopolymer sequence analysis together with GUI to work with biopolymer sequence databases. The tools include pairwise and multiple alignment, philogenetic tree construction and other.

GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation.

Bio::Prospect:: is a Perl API to the PROSPECT threading application. The modules provide for program execution, results parsing, multiple sequence alignments inferred from pairwise sequence-structure alignments, and rudimentary homology models.