Finding function in the unknown

Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.

Original languageEnglish (US)
Title of host publicationProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editorslng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1098-1099
Number of pages2
ISBN (Electronic)9781467367981
DOIs
StatePublished - Dec 16 2015
Externally publishedYes
EventIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States
Duration: Nov 9 2015Nov 12 2015

Publication series

NameProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Other

OtherIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
CountryUnited States
CityWashington
Period11/9/1511/12/15

Keywords

  • RNA-seq
  • comparative gene expression
  • de novo transcriptomics

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