mtDNAprofiler is a web program which enables users to analyze and compare mtDNA sequences whether they are indicated as FASTA format or as a difference to revised Cambridge Reference Sequence (rCRS).
Jnomics is a cloud-scale sequence analysis suite designed to help meet the computational challenges presented by the continuing revolution in massively parallel DNA sequencing technologies.
Jnomics-A cloud-scale sequence analysis suite.
Matt Titmus, Sneh Lata, Eric Antonious, James Gurtowski, W. Richard McCombie, and Michael Schatz
Genome Informatics, Cold Spring Harbor NY, Nov 3, 2011.
Seqtools is a large collection of tools for basic and advanced analyses of nucleotide and protein sequences. The tools are wrapped into a common user interface making handling, storage, retrieval and viewing the results easy and logical. A seqtools project can accommodate many thousand sequences making unattended batch analyses like database searching at NCBI painless with the robust search engine included in seqtools.
EGene is a generic, flexible and modular pipeline generation system that makes pipeline construction a modular job. EGene allows for third-party programs to be used and integrated according to the needs of distinct projects and without any previous programming or formal language experience being required.
Coed is a visual tool to facilitate pipeline construction and documentation.
SBSPKS is a webserver for carrying out sequence and structure based analysis of Polyketide Synthases, an important family of multifunctional megasynthases involved in the biosynthesis of a variety of pharmaceutically important secondary metabolites. The knowledge base for development of SBSPKS is derived from a comprehensive bioinformatics analysis of the sequence and structural features of a large number of experimentally characterized PKS gene clusters having known metabolic products and recently available crystal structures of PKS and FAS proteins.The interfaces for carrying out various tasks by SBSPKS are organized as three major functional units, namely NRPS_PKS, Model_3D_PKS and Dock_Dom_Anal .
RNASEQR is a nucleotide sequence mapper/aligner and is designed specifically for RNA-seq data analysis. It takes advantage of annotated transcripts and genomic reference sequences to obtain high quality mapping/alignment results.
(1) eMOTIF-SEARCH: Given a protein sequence, the eMOTIF-SEARCH program suggests families of proteins to which the query sequence may belong. The eMOTIF-SEARCH program considers a protein sequence a potential member of a protein family, if the sequence contains discrete motif or motifs that have been generated from an ungapped multiple sequence alignment of known member sequences from that family.
(2) eMOTIF-MAKER: The eMOTIF-MAKER program converts an ungapped multiple sequence alignment into a set of Pareto-optimal discrete motifs for use by the eMOTIF-SEARCH program and the eMOTIF-SCAN program. The resulting set of motifs often reveals sub-families within the cluster of proteins that share the region of sequence similarity covered by the given ungapped multiple sequence alignment.
(3) eMOTIF-SCAN: Given a regular expression, the eMOTIF-SCAN program finds all the occurrences of that regular expression in a particular sequence database.