Hartwell Center/Applications and Research Tools/DNA/Protein Sequence Analysis

Bioinformatics / Research Computing
Applications/Research Tools

> DNA / Protein Sequence Analysis^{1,
2}

Lasergene
Staden Package
Phred/Phrap/Consed
RepeatMasker
MEME
Consensus
mpiBlast

ClustalX
Transfac Pro. 11.4
HMMER
SEQC
BLAT
EMBOSS

Lasergene
Comprehensive Software for DNA & Protein Sequence Analysis, Contig Assembly and Sequence Project Management (manual [PDF])

How to Transfer Data From Vector NTI to Lasergene (manual [PPT])

Staden Package (X-windows emulation) The Staden Package is a software package to perform most aspects of sequence analysis including DNA assembly, sequence analysis, sequence comparisons, library handling and searching. (hc-alpha)

Phred/Phrap/Consed
Phred reads DNA sequencer trace data trace from chromatogram files in the SCF, ABI, and ESD formats, calls bases and assigns quality values to the bases.Phrap uses the quality values for the bases (written in FASTA format files or PHD files) for sequence assembly program in order to increase the accuracy of the assembled sequence.
Consed is a unix-based graphical editor program for phrap sequence assemblies. (hc-alpha)

RepeatMasker (command line)
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns) (hc-alpha)

MEME (command line)
MEME is a tool for discovering conserved motifs in a group of related DNA or protein sequences. (hc-alpha, hc-onyx, cluster)

Consensus (command line)
This program determines conserved patterns in unaligned DNA sequences. The algorithm is based on a matrix representation of consensus patterns (hc-alpha, cluster)

mpiBlast
MPIBlast is a freely available open source parallelization of NCBI BLAST. mpiBLAST segments the BLAST database and distributes it across cluster nodes, permitting BLAST queries to be processed on many nodes simultaneously. (cluster)

ClustalX (X-windows emulation)
Clustal X is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. (cluster)

New! Transfac Professional Transfac is a database on eukaryotic cis-acting regulatory DNA elements and trans-acting factors. It covers the whole range from yeast to human. (web)

HMMER (command line)
HMMER is a freely distributable implementation of profile HMM (hidden Markov models) software for protein sequence analysis. Profile HMMs can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. The current version is HMMER 2.3.1 (13 June 2003). (cluster)

SeqC
Sequence Format Conversion Application (web)

BLAT (command line)
Blast Like Alignment Tool (or BLAT), developed by Jim Kent at UCSC, is a stand-alone fast sequence search tool especially for sequences very large in size. It allows rapid detection of location of genes on chromosomes and the number of ORF in each gene. (cluster)

EMBOSS
The European Molecular Biology Open Software Suite (or EMBOSS) is a package of high-quality free software for DNA/Protein sequence analysis. It has a collection of around 100 applications to do sequence alignment, rapid database searching, protein motif detection, domain analysis, nucleotide codon usage, pattern-matching, and repeats analysis etc. (cluster)

¹Please contact your Local Support Provider (LSPs) to have any of these applications installed on your system. Click on the link below for a complete listing of the LSPs and their contact information: http://www.hartwellcenter.org/bio_rescom/clientSer/contactlsp.php

²To establish an account on a computer system, please fill out the Account Request Form and return to Bioinformatics (room D1010, first floor DTRT).