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PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome

机译：PIPEMicroDB：木豆基因组的微卫星数据库和引物生成工具

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Molecular markers play a significant role for crop improvement in desirable characteristics, such as high yield, resistance to disease and others that will benefit the crop in long term. Pigeonpea (Cajanus cajan L.) is the recently sequenced legume by global consortium led by ICRISAT (Hyderabad, India) and been analysed for gene prediction, synteny maps, markers, etc. We present PIgeonPEa Microsatellite DataBase (PIPEMicroDB) with an automated primer designing tool for pigeonpea genome, based on chromosome wise as well as location wise search of primers. Total of 123 387 Short Tandem Repeats (STRs) were extracted from pigeonpea genome, available in public domain using MIcroSAtellite tool (MISA). The database is an online relational database based on ‘three-tier architecture' that catalogues information of microsatellites in MySQL and user-friendly interface is developed using PHP. Search for STRs may be customized by limiting their location on chromosome as well as number of markers in that range. This is a novel approach and is not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of selected markers with left and right flankings of size up to 500 bp. This will enable researchers to select markers of choice at desired interval over the chromosome. Furthermore, one can use individual STRs of a targeted region over chromosome to narrow down location of gene of interest or linked Quantitative Trait Loci (QTLs). Although it is an in silico approach, markers' search based on characteristics and location of STRs is expected to be beneficial for researchers. Database URL: http://cabindb.iasri.res.in/pigeonpea/
机译：分子标记在作物改良方面具有重要作用，具有理想的特性，例如高产量，抗病性和长期有益于作物的其他特性。木豆（Cajanus cajan L.）是由ICRISAT（印度海德拉巴）领导的全球财团最近对豆科植物进行测序的产品，并已进行了基因预测，同义图，标记等的分析。我们提供了带有自动引物设计的PIgeonPEa微卫星数据库（PIPEMicroDB）木豆基因组的工具，基于染色体以及引物的位置搜索。从木豆基因组中提取了总共123387个短串联重复序列（STR），可使用MIcroSAtellite工具（MISA）在公共领域获得。该数据库是基于“三层体系结构”的在线关系数据库，该数据库在MySQL中对微卫星信息进行分类，并且使用PHP开发了用户友好的界面。可以通过限制STR在染色体上的位置以及该范围内的标记数来定制STR的搜索。这是一种新颖的方法，尚未在任何现有标记数据库中实现。该数据库还附加了Primer3，用于选择标记的引物设计，左右标记的大小不超过500 bp。这将使研究人员能够在染色体上的所需间隔内选择标记。此外，可以使用染色体上目标区域的单个STR来缩小目标基因或链接的数量性状基因座（QTL）的位置。尽管这是一种计算机方法，但基于STR的特征和位置的标记搜索有望对研究人员有所帮助。数据库URL：http://cabindb.iasri.res.in/pigeonpea/

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