Bioinformatics Facility

Services

The Bioinformatics Facility provides Wistar scientists with access to a wide variety of bioinformatics and computational biology tools, programs and analysis services.

Bioinformatics Facility services can be grouped into three categories:

1. Provide a suite of scientific computing resources including databases, programs, and website to meet the needs of Wistar investigators

2. Develop custom scientific computing tools

3. Data analysis and modeling, consultation, and training

The Bioinformatics Facility website (http://bioinfo.wistar.org) serves as the primary portal to specialized computational resources provided by the facility. Researchers may also obtain individual accounts on facility servers to gain access to non-web based scientific software which is primarily used for molecular modeling, CPU-intensive and/or large-scale batch processing.

For service policies and pricing information, see the Bioinformatics Facility website (http://bioinfo.wistar.org) or contact John J. Rux

Available tools:

Sequence Analysis
Wistar Local Blast Server - Standalone wwwBlast server (NCBI)

The Wistar local blast server provides access to a local version of the NCBI BLAST family of programs. The interface is similar to that used at NCBI's web site. Sequence databases from NCBI as well as custom in-house databases are maintained and accessed locally.

BLAST--An efficient sequence search algorithm.

blastp - compares an amino acid query sequence against a protein sequence database.

blastn - compares a nucleotide query sequence against a nucleotide sequence database.

blastx - compares a nucleotide query sequence translated in all reading frames against a protein sequence database.

tblastn - compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.

tblastx - compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

MegaBlast--Searches for large DNA sequence by querying with multiple smaller subsections. Implements a greedy algorithm for the DNA sequence gapped alignment search.

PSI/PHI Blast--Searches a profile against a database of sequences. An iterative search is performed by PSI-BLAST (Position-Specific Iterated BLAST) in which sequences found in one round of searching are used to build a score model for the next round of searching. PHI-BLAST (Pattern-Hit Initiated BLAST) is a search program that combines matching of regular expressions with local alignments surrounding the match.

RPS BlastCSearches a query sequence against a database of conserved domains, motifs, profiles, or HMMs.

WBlast2 sequences--This tool produces the alignment of two given sequences using BLAST engine for local alignment.

XMLBlast--Performs a Blast search and returns output in XML format.

Blastall--A command-line version of the Blast programs.

PromoterDB--Custom database of potential promoter sequences searchable with the local Blast server.

MSPcrunch--A blast data post processor. It is used to selectively find hits at the 'twilight' area of blast searches and discriminate away ones of little statistical significance. It does this by looking for compositional bias and adjacency criteria.

RepeatMasker--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.

FPC--An interactive program for assembling contigs from fingerprint data (e.g. a single set of fragments per clone).

Genescan--A general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants.

Clustalx--Performs multiple sequence alignment and generates phylogenetic trees.

MSA--multiple sequence alignment program.

Phylip-A package of programs for inferring phylogenies and carrying out certain related tasks.

Readseq--Tool for converting sequence from one format into another.

GCG, Seqlab, SeqWeb--Collection of programs used to analyze or manipulate DNA and protein sequence data.

Sequence Assembly
Sequence Assembly tools from the University of Washington.

Phred--Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.

Phrap--Program for assembling shotgun DNA sequence data. It is strongly recommended that phrap be used in conjunction with the base calls and base quality values produced by the basecaller, phred; and with the sequence editor/assembly viewer, consed

Consed--Sequence editor/assembly viewer. To view output of Phrap.

SWAT--An efficient implementation of the Smith-Waterman algorithm for comparing any two sets of (long or short) DNA sequences

Protein Structure Analysis

Procheck--Consists of programs for assessing the overall geometrical quality of protein structures.

Promotif--Provides details of the location and types of structural motifs in proteins of known structure by analysis of Brookhaven format coordinate files.

CNSsolve--The program has been designed to provide a flexible multi-level hierarchical approach for the most commonly used algorithms in macromolecular structure determination.