Bioinformatics support

Overview

UITS supports researchers who do biological computing, particularly in the areas of genomics, cell biology, and molecular biology. Support is provided in the forms of application support, technical support, and software development. Application support includes testing and licensing of software that is broadly useful across academic departments that analyze molecular data, including biology, medicine, and anthropology. Technical support includes consulting with regard to data management and choice of algorithms and statistical methods of data analysis. Software development includes investment of time assisting researchers developing software that poses challenges for which they lack resources to complete in a timely fashion.

Services

Software on UITS computer systems

UITS provides bioinformatics software on the the Quarry cluster and on Big Red. Quarry is for long-running single-processor programs, programs that require large amounts of memory, and parallel programs that require memory that is shared by many processors (SMP). Big Red is configured for massively parallel computing. To request software for general use on research systems, submit a software request form.

The following bioinformatics software is available:

• BLAST can be used to query hundreds to tens of thousands of molecular sequences against sequence databases. For details, see BLAST sequence searching on Big Red.
  
  
• CAP3 is a sequence assembly program. For details, see Using CAP3 on Big Red at IU.
  
  
• ClustalW aligns multiple sequences. A parallel version is available on Big Red; see Running ClustalW on Big Red.
  
  
• EMBOSS/wEMBOSS is a set of sequence analysis applications that use GCG libraries to extend the functionality of the GCG Package. wEMBOSS is the web interface of the EMBOSS. EMBOSS command line applications run on the Quarry cluster. The wEMBOSS interface is available on the Discern server (discern.uits.iu.edu). For details, see On Quarry, what are EMBOSS and wEMBOSS, and how can I use them?
  
  
• FASTA searches databases for sequences that are similar to a set of query sequences. The parallel version of FASTA is available on Big Red. For more, see FASTA programs on Big Red.
  
  
• fastDNAml generates phylogenetic trees from molecular data using maximum likelihood methods. The program implements Felsenstein's likelihood methods and Olson's search algorithm. This implementation was parallelized by the UITS High Performance Applications team. For more, see Maximum likelihood analysis of phylogenetic data.
  
  
• GARLI conducts phylogenetic searches on aligned sequences using maximum likelihood criteria. It supports codon- and amino-acid-based models in addition to standard nucleotide models. See What is GARLI, and how can I use it on Quarry?
  
  
• IMPUTE is a program for predicting unobserved genotypes based upon observed/known haplotypes in genome-wide case-control studies. See What is IMPUTE, and how do I use it on Quarry at IU?
  
  
• MACH is a Markov-chain-based haplotyper. See What is MACH, and how do I use it on Quarry at IU?
  
  
• MEME detects patterns in nucleotide and protein sequences and efficiently uses multiple processors. See Using MEME on Big Red at IU.
  
  
• MIGRATE uses genotypes of individuals to form clusters that represent populations, assign individuals to populations, and describe genotypes of individuals in terms of populations from which they were derived. It applies maximum likelihood and Bayesian analysis. See What is MIGRATE, and how can I use it on Quarry?
  
  
• MPI-HMMER creates and queries sets of hidden Markov models that describe molecular sequences. This port of HMMER includes parallel versions of hmmpfam and hmmsearch and is available on Big Red. See Using MPI-HMMER on Big Red at IU.
  
  
• MrBayes estimates evolutionary trees using Bayesian methods. It has been compiled to use multiple processors. For more, see On Big Red, how do I submit batch jobs that run MrBayes?
  
  
• MULTICLUSTAL optimizes multiple sequence alignments by searching for the best alignment parameters. See Running MULTICLUSTAL on Big Red at IU.
  
  
• PAUP estimates evolutionary trees and is available on the Quarry cluster. For details, see Using PAUP on Quarry at IU.
  
  
• PHYLIP is a well known package for phylogenetic inferences. It is available on the Quarry cluster. For help, see the program documentation and Using PHYLIP on Quarry at IU.
  
  
• Phrap/Cross_match/Swat is a set of programs for DNA analysis. It is available on Big Red. Phrap assembles shotgun DNA sequence data. Cross_match compares any two DNA sequence sets. Swat searches DNA/protein sequences, or a query profile, against a sequence database. For more, see Using Phrap/Cross_match/Swat on Big Red.
  
  
• PLINK is a tool set for genome association study. See What is PLINK, and how do I use it on Quarry at IU?
  
  
• RepeatMasker is a program for finding and removing repeated low-complexity regions in DNA sequences. It's available on Big Red. For more, see Using RepeatMasker on Big Red.
  
  
• structure is a program that can cluster individuals based on their genotypes and can assign individuals to clusters (populations) based on their genotypes. It is installed on Quarry. For more, see What is structure, and how do I use it on Quarry?
  
  
• TREE-PUZZLE estimates phylogenetic trees from sequence data using maximum likelihood methods. A parallel version is available on Big Red. For details, see Using TREE-PUZZLE on Big Red at IU.

Data

Centralized Life Sciences Data (CLSD) provides an access point through which a number of public data sources can be queried programmatically using SQL. It is also possible to phrase NCBI BLAST searches as SQL queries. For more about CLSD, see Research Technologies at Indiana University.

Consulting is available to help researchers find solutions to bioinformatics computing problems. For assistance, email BIOS.

This document was developed with support from the National Science Foundation (NSF) under Grant No. 0503697 to the University of Chicago and subcontracted to Indiana University. Additional support was provided by IU through its participation in the TeraGrid, which is supported by the NSF under Grants No. 0833618, SCI451237, SCI535258, and SCI504075. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

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