Bioinformatics

SBGrid supports 23 bioinformatics software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

Aline

- an interactive perl/tk application that can read common sequence alignment formats that the user can then alter, embellish, markup, etc. to produce the kind of sequence figure commonly found in biochemical articles. Developed by Charlie Bond and Alex Schüttelkopf.

yes yes yes

Alscript

- a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. Alscript does not support point-and-click, but has a scripting language to allow complex effects.

yes yes

AMPS

- a suite of programs designed for the alignment of multiple protein sequences and flexible pattern matching.

yes yes yes

BLAST

- (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

yes yes yes

breseq

- a computational pipeline for finding mutations relative to a reference sequence in short-read DNA.

yes yes yes

Clustal

- a general purpose multiple sequence alignment program for DNA or proteins.

yes yes yes

EMBOSS

- integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

yes yes yes

FASTA

- a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. First described (as FASTP) by David J. Lipman and William R. Pearson in 1985.

yes yes yes

Jalview

- a multiple sequence alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.

yes yes yes

MAFFT

- a multiple sequence alignment program. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.

yes yes yes

Matt

- a multiple protein structure alignment program. It uses local geometry to align segments of two sets of proteins, allowing limited bends in the backbones between the segments.

yes yes yes

MOLPHY

- (MOLecular PHYlogenetics) is a computer program package for molecular phylogenetics.

yes yes yes

MUSCLE

- (multiple sequence comparison by log-expectation) is a public domain multiple alignment software for protein and nucleotide sequences.

yes yes yes

NETBLAST

- NETBLAST is a simple command-line program that allows you to submit a single file of FASTA sequences over an internet connection to the NCBI BLAST databases. Searches are submitted through the client to the NCBI servers and do not need to download the databases locally (also called netblast and blastcl3).

yes yes yes

PHYLIP

- a free package of software programs for inferring phylogenies.

yes yes yes

Primer3

- a widely used program that designs PCR primers (PCR = "Polymerase Chain Reaction"). Primer3 can also design hybridization probes and sequencing primers.

yes yes yes

PROBCONS

- an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

yes yes yes

PSIPRED

- uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.

yes yes yes

SAM

- a collection of tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. The model states can be viewed as representing the sequence of columns in a multiple sequence alignment, with provisions for arbitrary position-dependent insertions and deletions in each sequence. The models are trained on a family of protein or nucleic acid sequences using an expectation-maximization algorithm and a variety of algorithmic heuristics. A trained model can then be used to both generate multiple alignments and search databases for new members of the family.

yes yes yes

SCC

- a suite of programs for sequence alignment including: aln, swg, prrn, phyln and makmdm. aln: Pairwise alignment of biological sequences supporting spliced alignment procedures. swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm. Currently spliced alignment is not supported. Profile version is very slow. prrn: global multiple alignment of a set of protein or DNA sequences by doubly nested iterative refinement method. phyln: UPGMA or NJ method to make a phylogenetic tree from a multiple alignment. makmdm: constructs binary PAM matrices. Must be run once before the first run of aln, swg or prrn.

yes yes yes

SSAHA2

- (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.

yes yes yes

Staden

- a set of DNA sequence assembly, editing and analyzing tools. Developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK

yes yes yes

T-Coffee

- a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).

yes yes yes