Bioinformatics

From Innovita

Bioinformatics

InnoVita's scientists have extensive experience in the following areas:

Scientific Application Programming

   *  Languages: Perl, Java, PHP, PL/SQL, Oracle,  MS SQL and MySQL
   * Database design and backend application development using 
     ERWin, PL/SQL, Oracle,  MS SQL and MySQL.
   * Front end web application development using Perl, Java, PHP and HTML.

Real-time PCR Assay Design

   *  Design of primers and fluorescent probes including data.
   *  Sequences of primers and probes.
   *  BLAST data to demonstrate the design specificity.
   *  Oligonucleotide alignment on target template.
   *  Amplification protocol recommendations (thermal cycling and buffer conditions).

Genome Assembly and Annotation Services

   * Assembly of sequences generated by traditional shortgun sequencing.
   * Assembly of short sequences generated using 454 Life Sciences Instrument System,  
     in combination with sequences from shortgun sequencing.
   * Annotation of microbial genomes.
   * Install and configure linux server
   * Install and configure bioinformatics software including Manatee, ART, ACT, Glimmer,
     MUMer, AMOS, BAMBUS. Celera Assembler, PCAP, Phrap, Consed on linux server

Comparative Genome Analysis

   *  ACT,  MUMer

DNA and Protein Homology and Similarity Searches

   * BLAST Searches of all major sequence databases such as NCBI and EMBL
   * FASTA Searches
   * HMMER Searches
   * SRS - Sequence Retrieval System
   * MPsrch
   * Scanps

Sequence Analysis

   * Align: Pairwise global and local alignment
   * ClustalW: Multiple sequence alignments
   * GeneWise: Compares a protein sequence or a protein profile HMM to a DNA sequence.
   * TkDCSE

Protein Functional Analysis

   * CluSTr Search
   * FingerPRINTScan
   * GeneQuiz
   * InterProScan
   * PPSearch
   * Radar
   * Protein ab initio structure prediction
   * Protein homology modeling

Phylogenetic analysis

   * PAUP
   * Phylip
   * Molphy
   * Puzzle

Computer modeling of dynamic biological systems

   * Structure-function analysis
   * Computational and combinatorial chemistry

Biomedical database design, analysis, and development

   * UML modeling
   * Database schema design and implementation
   * Database transformation and loading
   * User interface development using Java (MVC web interface) or .Net

Microarray data analysis

   * SAS
   * S-Plus
   * R
   * Metlab

In addition, we are proficient in using the following software for microarray data analysis, image processing and data management:

   * Bioconductor
   * Partek Pro
   * DChip
   * ArrayTools
   * SAM
   * Affymetrix GeneChip
   * CLUSTER
   * CLUSFAVOR
   * GENE-CLUSTER
   * SMA
   * GENEX

Semantic web and ontology development

   * Development of biomedical ontologies
   * Data integration using ontology
   * Data mining using ontology