Herrera-Galeano Jesus Enrique, Frey Kenneth G, Cer Regina Z, Mateczun Alfred J, Bishop-Lilly Kimberly A, Mokashi Vishwesh P
Naval Medical Research Center-Frederick, 8400 Research Plaza, Frederick, MD, USA.
Source Code Biol Med. 2014 Mar 31;9(1):7. doi: 10.1186/1751-0473-9-7.
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.
We have created BLASTPLOT, a PERL module to quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets.
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.
在过去十年中，新一代测序（NGS）技术的发展产生了前所未有的大量测序数据，同时也具备了快速对感兴趣的样本进行测序的能力。对NGS数据进行基于读段的BLAST分析是一种常见的操作，尤其是在宏基因组样本的情况下。然而，覆盖度通常不足以进行从头组装。这种基于读段的分析常常会引发这样一个问题：与同一序列比对上的读段是如何分布的。同样的问题也适用于微阵列实验中引物或探针的制备。尽管有几个软件包可以实现与参考序列相关的DNA片段可视化，但在大多数情况下，它们每次只能可视化一个参考序列，并且需要为每个片段捕获屏幕截图。这样的过程可能既繁琐又耗时。该领域需要一种能够自动捕获所有感兴趣片段的覆盖度图的解决方案。
我们创建了BLASTPLOT，这是一个PERL模块，用于快速绘制短序列（引物、探针、读段）与参考目标的BLAST结果。
BLASTPLOT是一个易于使用的PERL模块，它能够为与BLAST结果集相关的所有参考序列生成PNG图形。
