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Sequence analysis encompasses the use of various bioinformatics methods to determine the biological function and/or structure of genes and the proteins they code for Next-generation sequencing technologies are revolutionising genomics and their effects are becoming increasingly widespread.
The first of the "next-generation" sequencing technologies, MPSS was developed in the 1990s. MPSS was a bead-based method that used a complex approach of adapter ligation followed by adapter decoding, reading the sequence in increments of four nucleotides; this method made it susceptible to sequence-specific bias or loss of specific sequences. Because the technology was so complex, MPSS was only performed 'in-house' .when the merger with Solexa later led to the development of sequencing-by-synthesis, a more simple approach with numerous advantages, MPSS became obsolete. However, the essential properties of the MPSS output were typical of later "next-gen" data types, including hundreds of thousands of short DNA sequences. In the case of MPSS, these were typically used for sequencing cDNA for measurements of gene expression levels.
Our extensive experience with a wide range of sequences allows us to select/recommend the protocols needed to determine sequence analysis. Sequence availability is not always ideal. The sequence may be in limited length or may have been collected in sub-optimal conditions. We have successfully analyzed many sequences like these, optimizing protocols depending on the situation.
Our past experiences
The sequence may be in limited length or may have been collected in sub-optimal conditions. We have successfully analyzed many sequences like these, optimizing protocols on depends.
- Currently working with next-generation sequence (GS FLX 454, Roche) Data Analysis team.
- Automated Pipeline Development for the next-generation sequencing (GS FLX 454, Roche) data.
- Implementing Next-generation sequencing data analysis tools and file formats: SFF files, Fastq files, SAM/BAM, pileup, UCSC genome browser, SNP calling tools VarScan, Samtools, Picard, Annovar.
- Actively involved in development of Next-Gen Sequencing data analysis pipeline.
- Implemented reference-mapping pipelines, starting with miRNA profiling, for Solid-ABI and Illumina reads data.
- Involved in algorithm development and scripting for various modules within these pipelines, and implementation of one such pipeline in two separate client services.
- Processing and reference mapping of different rice reads for small RNA, and miRNA profile with read mapping to rice genome.
- Trimming and mapping of Mouse and Human; IlluminamiRNA specific reads to find known miRNAs.
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