Dna Sequence Analysis

The seqlogo tool in the bioinformatics toolbox generates good sequence logos, unfortunately they cannot be incorporated into other programs. This routine generates DNA sequence logos as raw images. Platforms: Matlab

Seqlib is a Python module and application package for population genetics (and more). It allows processing, analyzing and simulating biological sequences. It is specifically designed for automated large-scale sequence analysis. Main features: * Fasta-centered input and output, format... Platforms: Mac

MutantMaker helps researchers performing site directed mutagenesis screen their potential mutants with restriction enzyme digests rather than costly sequencing. The oligonucleotide sequences suggested by MutantMaker will create or destroy restriction sites while both creating the desired mutant... Platforms: Mac

DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other... Platforms: Windows

WinBlast is a handy, easy to use application specially designed to offer you a graphical front-end for NCBI BLAST. Platforms: Windows

DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other... Platforms: Linux

DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other... Platforms: Mac

Seqwog is a small, command prompt application specially designed to help you find frequent sequences without gaps in their occurrences. That is, the items of the frequent subsequences must always be consecutive in the underlying transactions. There must not be other items interspersed between... Platforms: Windows

Plasmid Entry Form is a simple, easy to use application designed to help you create plasmid database forms for BGME lab. This program presents user with a data entry form for entering plasmid information and automatically converts DNA sequence to protein, aligns it, and creates text output file. Platforms: Windows

HapEdit is an instrument that's been specially built in order to help the user assess the accuracy of haplotype assembly. This is done using the next-generation sequencing technologies. HapEdit is a tool that was created with the help of the Java programming language and can run on multiple... Platforms: Windows

Molecular-based diagnostic assays are the gold standard for infectious diseases today, since they allow a rapid and sensitive identification and typing of various pathogens. While PCR can be designed to be specific for a certain pathogen, a subsequent sequence analysis is frequently required... Platforms: Windows

OrientationChecker is a simple, Java based application specially designed to help you check and alter the orientation of 16S rRNA gene sequences. Platforms: Windows

The BioPHP Project is a non-profit, open source software project that aims to extend the PHP scripting language so it can be used to develop bioinformatics applications. BioPHP is NOT a bioinformatics application. Rather, it is a collection of tools to help PHP developers write bioinformatics... Platforms: Windows, Mac, *nix, PHP, BSD Solaris

This application is an interactive simulation of gene expression that allows the user to: Explore a sample gene: Explore the correspondence between DNA, pre-mRNA, mature mRNA, and protein Map the functional elements of a gene. Create mutations in a gene and explore their effects. Design... Platforms: Mac

An exceptional tool for drawing publication and vector catalog quality maps and designing cloning experiments. SimVector: Software to draw accurate plasmid maps Exceptional Publication Quality Plasmid Maps Whether you are a catalog company selling engineered plasmids or conducting restriction... Platforms: Mac

alculate the normalized partial energy sequence (NPES) for a given signal vector X.If a particular transform is capable of capturing the key features of a signal in few coefficients, the NPES will approach unity for relatively quickly.Ref: Percival and Walden, Wavelet Methods for Time Series... Platforms: Matlab

Bio::Restriction::Enzyme is a single restriction endonuclease (cuts DNA at specific locations). SYNOPSIS # set up a single restriction enzyme. This contains lots of # information about the enzyme that is generally parsed from a # rebase file and can then be read back use... Platforms: *nix

UGENE is a comprehensive genome analysis suite that features multiple sequence alignment and a complex HMM builder and search module. for WindowsAll Platforms: Windows

CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options. Bioinformatics features in CLC Sequence Viewer Multiple alignment of DNA, RNA, and... Platforms: Windows

BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions. Platforms: Mac