A sensitive short read homology search tool for paired-end read sequencing data

BMC Bioinformatics
Prapaporn Techa-AngkoonJikai Lei

Abstract

Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. While the state-of-the-art tool HMMER has achieved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads declines rapidly. The low sensitivity on short read homology search can lead to inaccurate domain composition and abundance computation. Our experimental results showed that half of the reads were missed by HMMER for a RNA-Seq dataset. Thus, there is a need for better methods to improve the homology search performance for short reads. We introduce a profile homology search tool named Short-Pair that is designed for short paired-end reads. By using an approximate Bayesian approach employing distribution of fragment lengths and alignment scores, Short-Pair can retrieve the missing end and determine true domains. In particular, Short-Pair increases the accuracy in aligning short reads that...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·S Karlin, S F Altschul
Jan 10, 2003·Nucleic Acids Research·Daniel H HaftOwen White
Dec 31, 2005·Nucleic Acids Research·Robert D FinnAlex Bateman
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Sep 19, 2009·Nucleic Acids Research·Folker MeyerAlex Rodriguez
Oct 29, 2010·Genome Research·Gerton Lunter, Martin Goodson
May 31, 2011·Nucleic Acids Research·Thomas LingnerPeter Meinicke
Jun 21, 2011·Bioinformatics·Yu PengFrancis Y L Chin
Sep 8, 2011·Nature Reviews. Genetics·Jeffrey A Martin, Zhong Wang
Nov 1, 2011·PLoS Computational Biology·Sean R Eddy
Dec 1, 2011·Nucleic Acids Research·Marco PuntaRobert D Finn
Dec 16, 2011·The ISME Journal·Chris L DupontJ Craig Venter
Jul 24, 2012·Nucleic Acids Research·Toshiaki NamikiYasubumi Sakakibara
Jan 17, 2013·Genome Biology·Todd J TreangenMihai Pop
Feb 16, 2013·Bioinformatics·Anish Man Singh Shrestha, Martin C Frith
Mar 14, 2013·Biology & Philosophy·Iratxe ZarraonaindiaJack A Gilbert
Nov 30, 2013·Nucleic Acids Research·Robert D FinnMarco Punta
Jul 24, 2015·Genesis : the Journal of Genetics and Development·Tanya Z BerardiniEva Huala

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-Seq

Software Mentioned

Pair
Bowtie
Short
HMMER
EBI portal
Assembler
HMMER GA cutoff
SAT
TIGRFAM
IMG

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.