BLASTPLOT: A PERL module to plot next generation sequencing NCBI-BLAST results

Jesus E. Herrera-Galeano, Kenneth G. Frey, Regina Z. Cer, Alfred J. Mateczun, Kimberly A. Bishop-Lilly, Vishwesh P. Mokashi

Research output: Contribution to journalArticle

Abstract

Background: The development of Next Generation Sequencing (NGS) during the last decade has created an unprecedented amount of sequencing data, as well as the ability to rapidly sequence specimens of interest. Read-based BLAST analysis of NGS data is a common procedure especially in the case of metagenomic samples. However, coverage is usually not enough to allow for de novo assembly. This type of read-based analysis often creates the question of how the reads that align to the same sequence are distributed. The same question applies to preparation of primers or probes for microarray experiments. Although there are several packages that allow the visualization of DNA segments in relation to a reference, in most cases they require the visualization of one reference at a time and the capture of screen shots for each segment. Such a procedure could be tedious and time consuming. The field is in need of a solution that automates the capture of coverage plots for all the segments of interest.Results: We have created BLASTPLOT, a PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets.Conclusions: BLASTPLOT is a simple to use PERL module that allows the generation of PNG graphs for all the reference sequences associated with a BLAST result set.

Original languageEnglish (US)
Article number7
JournalSource Code for Biology and Medicine
Volume9
Issue number1
DOIs
StatePublished - Mar 31 2014
Externally publishedYes

Fingerprint

Visualization
Metagenomics
Microarrays
DNA
Experiments
Sequencing
Module

Keywords

  • BLAST
  • Graph
  • NGS
  • Package
  • PERL
  • Plot
  • Primer
  • Probe
  • Reads
  • Sequencing

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Information Systems and Management
  • Health Informatics

Cite this

Herrera-Galeano, J. E., Frey, K. G., Cer, R. Z., Mateczun, A. J., Bishop-Lilly, K. A., & Mokashi, V. P. (2014). BLASTPLOT: A PERL module to plot next generation sequencing NCBI-BLAST results. Source Code for Biology and Medicine, 9(1), [7]. https://doi.org/10.1186/1751-0473-9-7

BLASTPLOT : A PERL module to plot next generation sequencing NCBI-BLAST results. / Herrera-Galeano, Jesus E.; Frey, Kenneth G.; Cer, Regina Z.; Mateczun, Alfred J.; Bishop-Lilly, Kimberly A.; Mokashi, Vishwesh P.

In: Source Code for Biology and Medicine, Vol. 9, No. 1, 7, 31.03.2014.

Research output: Contribution to journalArticle

Herrera-Galeano, JE, Frey, KG, Cer, RZ, Mateczun, AJ, Bishop-Lilly, KA & Mokashi, VP 2014, 'BLASTPLOT: A PERL module to plot next generation sequencing NCBI-BLAST results', Source Code for Biology and Medicine, vol. 9, no. 1, 7. https://doi.org/10.1186/1751-0473-9-7
Herrera-Galeano JE, Frey KG, Cer RZ, Mateczun AJ, Bishop-Lilly KA, Mokashi VP. BLASTPLOT: A PERL module to plot next generation sequencing NCBI-BLAST results. Source Code for Biology and Medicine. 2014 Mar 31;9(1). 7. https://doi.org/10.1186/1751-0473-9-7
Herrera-Galeano, Jesus E. ; Frey, Kenneth G. ; Cer, Regina Z. ; Mateczun, Alfred J. ; Bishop-Lilly, Kimberly A. ; Mokashi, Vishwesh P. / BLASTPLOT : A PERL module to plot next generation sequencing NCBI-BLAST results. In: Source Code for Biology and Medicine. 2014 ; Vol. 9, No. 1.
@article{e8e5e120aad4483b8cd9e89e501a4da7,
title = "BLASTPLOT: A PERL module to plot next generation sequencing NCBI-BLAST results",
abstract = "Background: The development of Next Generation Sequencing (NGS) during the last decade has created an unprecedented amount of sequencing data, as well as the ability to rapidly sequence specimens of interest. Read-based BLAST analysis of NGS data is a common procedure especially in the case of metagenomic samples. However, coverage is usually not enough to allow for de novo assembly. This type of read-based analysis often creates the question of how the reads that align to the same sequence are distributed. The same question applies to preparation of primers or probes for microarray experiments. Although there are several packages that allow the visualization of DNA segments in relation to a reference, in most cases they require the visualization of one reference at a time and the capture of screen shots for each segment. Such a procedure could be tedious and time consuming. The field is in need of a solution that automates the capture of coverage plots for all the segments of interest.Results: We have created BLASTPLOT, a PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets.Conclusions: BLASTPLOT is a simple to use PERL module that allows the generation of PNG graphs for all the reference sequences associated with a BLAST result set.",
keywords = "BLAST, Graph, NGS, Package, PERL, Plot, Primer, Probe, Reads, Sequencing",
author = "Herrera-Galeano, {Jesus E.} and Frey, {Kenneth G.} and Cer, {Regina Z.} and Mateczun, {Alfred J.} and Bishop-Lilly, {Kimberly A.} and Mokashi, {Vishwesh P.}",
year = "2014",
month = "3",
day = "31",
doi = "10.1186/1751-0473-9-7",
language = "English (US)",
volume = "9",
journal = "Source Code for Biology and Medicine",
issn = "1751-0473",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - BLASTPLOT

T2 - A PERL module to plot next generation sequencing NCBI-BLAST results

AU - Herrera-Galeano, Jesus E.

AU - Frey, Kenneth G.

AU - Cer, Regina Z.

AU - Mateczun, Alfred J.

AU - Bishop-Lilly, Kimberly A.

AU - Mokashi, Vishwesh P.

PY - 2014/3/31

Y1 - 2014/3/31

N2 - Background: The development of Next Generation Sequencing (NGS) during the last decade has created an unprecedented amount of sequencing data, as well as the ability to rapidly sequence specimens of interest. Read-based BLAST analysis of NGS data is a common procedure especially in the case of metagenomic samples. However, coverage is usually not enough to allow for de novo assembly. This type of read-based analysis often creates the question of how the reads that align to the same sequence are distributed. The same question applies to preparation of primers or probes for microarray experiments. Although there are several packages that allow the visualization of DNA segments in relation to a reference, in most cases they require the visualization of one reference at a time and the capture of screen shots for each segment. Such a procedure could be tedious and time consuming. The field is in need of a solution that automates the capture of coverage plots for all the segments of interest.Results: We have created BLASTPLOT, a PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets.Conclusions: BLASTPLOT is a simple to use PERL module that allows the generation of PNG graphs for all the reference sequences associated with a BLAST result set.

AB - Background: The development of Next Generation Sequencing (NGS) during the last decade has created an unprecedented amount of sequencing data, as well as the ability to rapidly sequence specimens of interest. Read-based BLAST analysis of NGS data is a common procedure especially in the case of metagenomic samples. However, coverage is usually not enough to allow for de novo assembly. This type of read-based analysis often creates the question of how the reads that align to the same sequence are distributed. The same question applies to preparation of primers or probes for microarray experiments. Although there are several packages that allow the visualization of DNA segments in relation to a reference, in most cases they require the visualization of one reference at a time and the capture of screen shots for each segment. Such a procedure could be tedious and time consuming. The field is in need of a solution that automates the capture of coverage plots for all the segments of interest.Results: We have created BLASTPLOT, a PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets.Conclusions: BLASTPLOT is a simple to use PERL module that allows the generation of PNG graphs for all the reference sequences associated with a BLAST result set.

KW - BLAST

KW - Graph

KW - NGS

KW - Package

KW - PERL

KW - Plot

KW - Primer

KW - Probe

KW - Reads

KW - Sequencing

UR - http://www.scopus.com/inward/record.url?scp=84897462596&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84897462596&partnerID=8YFLogxK

U2 - 10.1186/1751-0473-9-7

DO - 10.1186/1751-0473-9-7

M3 - Article

AN - SCOPUS:84897462596

VL - 9

JO - Source Code for Biology and Medicine

JF - Source Code for Biology and Medicine

SN - 1751-0473

IS - 1

M1 - 7

ER -