Data Mining for Simple Sequence Repeats in Oil Palm Expressed Sequence Tags

Expressed Sequence Tags or ESTs are small pieces of DNA sequence that are generated by sequencing either one or both ends of an expressed gene. ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on gene expression and regulation, and for constructing genome maps. Oil palm EST sequences as available in public domain are downloaded. They were grouped and made contigs using CAP3 and Phrap. Microsatellite repeats are located using 5 softwares (MISA, TRA, TROLL, SSRIT, SSR primer). Among the 5 methods MISA is found to be the best. It can elucidate the compound repeat also. Frequency and total number (202) of SSR were detected. Mononucleotide repeat is more abundant especially ‘A/T’ repeats in Oil palm. Flanking primers were designed using primer3, SSR primers. The results of the study are given as an online database ‘MEMCO’ to help Oil palm researchers

MiIP: The Monomer Identification and Isolation Program

Repetitive elements within genomic DNA are both functionally and evolutionarily informative. Discovering these sequences ab initio is computationally challenging, compounded by the fact that selection on these repeats is often relaxed; thus sequence identity between repetitive elements can vary significantly. Here we present a new application, the Monomer Identification and Isolation Program (MiIP), which provides functionality to both search for a particular repeat as well as discover repetitive elements within a larger genomic sequence. To compare MiIP’s performance with other repeat detection tools, analysis was conducted for synthetic sequences as well as several α21-II clones and HC21 BAC sequences. The primary benefit of MiIP is the fact that it is a single tool capable of searching for both known monomeric sequences as well as discovering the occurrence of repeats ab initio, per the user’s required sensitivity of the search. Furthermore, the report functionality helps easily facilitate subsequent phylogenetic analysis

Bioinformatics tools for development of fast and cost effective simple sequence repeat (SSR), and single nucleotide polymorphisms (SNP) markers from expressed sequence tags (ESTs)

The development of current molecular biology techniques has led to the generation of huge amount of gene sequence information under the expressed sequence tag (EST) sequencing projects on a large number of plant species. This has opened a new era in crop molecular breeding with identification and/or development of a new class of useful DNA markers called genic molecular markers (GMMs). These markers represent the functional component of the genome in contrast to all other random DNA markers (RMMs). Many recent studies have demonstrated that GMMs may be superior to RMMs for use in the marker assisted selection, comparative mapping and exploration of functional genetic diversity in the germplasms adapted to different environment. Therefore, identification of DNA sequences which can be used as markers remains fundamental to the development of GMMs. Amongst others; bioinformatics approaches are very useful for development of molecular markers, making their development much faster and cheaper. Already, a number of computer programs have been implemented that aim at identifying molecular markers from sequence data. A revision of current bioinformatics tools for development of genic molecular markers is, therefore, crucial in this phase. This mini-review mainly provides an overview of different bioinformatics tools available and its use in marker development with particular reference to SNP and SSR markers.Keywords: Genic molecular marker, simple sequence repeat (SSR), and single nucleotide polymorphisms (SNP) markers from expressed sequence tags (ESTs).African Journal of Biotechnology Vol. 12(30), pp. 4713-472

New softwares for automated microsatellite marker development

Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence ‘experiment file’ format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut

Terrier köpek normal ve tümörlü meme dokusu EST Kütüphanelerinden SSR’ların belirlenmesi

Dogs share a common environment with humans and knowledge of the specific dog breed diseases is very useful in developing a model for human cancer studies. ESTs represent part of the transcribed genome of an organism and are an important resource for identifying microsatellites. Simple Sequence Repeats (SSRs), or microsatellites, which contain repetitive DNA sequences, are among the most powerful genetic markers known. The development of EST-SSRs has become a fast, efficient, and low-cost option for genomic studies. In this study, to determine SSRs from EST libraryof mammary gland tissue of the Terrier dog that has 2304 ESTs; SSRIT and IMEx software, which have web-based versions and are easily accessible, were used. SSRIT finds motifs from 2 to 10 base lengths and adjusts the minimum number of repeats by eliminating single nucleotide motifs. IMEx finds perfect and imperfect microsatellites separately. It can find motifs of different lengths from 1 to 6 and the minimum number of repeats can be set. In addition, the appropriate primer for the desired SSR region can be designed. The 2, 3, 4, 5 and 6 nucleotide motifs were found for normal tissue ESTs whereas 5 nucleotide motifs were not found for tumoral tissue ESTsKöpekler, insanlarla ortak bir çevreyi paylaşır ve belirli köpek ırklarının hastalıkları hakkında bilgi, insan kanser çalışmaları için bir model geliştirmede çok yararlıdır. EST'ler, bir organizmanın transkribe edilen genomunun bir parçasını temsil eder ve mikrosatellitleri tanımlamak için önemli bir kaynaktır. Tekrarlayan DNA dizilerini içeren Basit Dizi Tekrarları (SSR'ler) veya mikrosatellitler, bilinen en güçlü genetik belirteçler arasındadır. EST-SSR'lerin gelişimi, genomik çalışmalar için hızlı, verimli ve düşük maliyetli bir seçenek haline gelmiştir. Bu çalışmada, 2304 EST içeren Terrier köpeğin meme bezi dokusunun EST koleksiyonundan SSR'lerin belirlenmesi için; Web tabanlı sürümleri olan ve kolayca erişilebilen SSRIT ve IMEx yazılımları kullanılmıştır. SSRIT, 2 ila 10 baz uzunluğundaki motifleri bulur ve tekli nükleotid motiflerini ortadan kaldırarak minimum tekrar sayısını ayarlar. IMEx mükemmel ve kusurlu mikrosatellitleri ayrı ayrı bulur. Farklı uzunluklarda 1 ile 6 arasındaki motifleri bulabilir ve minimum tekrar sayısı ayarlanabilir. Ek olarak, istenen SSR bölgesi için uygun primer tasarlanabilir. Normal doku EST'leri için 2, 3, 4, 5 ve 6 nükleotidli motifler bulunurken, tümörlü doku EST'leri için 5 nükleotidli motif bulunamamıştır

Microsatellite markers for the Indian golden silkmoth, Antheraea assama (Saturniidae: Lepidoptera)

Antheraea assama, an economically important and scientifically unexplored Indian wild silkmoth, is unique among saturniid moths. For this species, a total of 87 microsatellite markers was derived from 35 000 expressed sequence tags and a microsatellite-enriched sub-genomic library. Forty individuals collected from Tura and West Garo Hills region of Northeast India were screened for each of these loci. Ten loci from expressed sequence tags and one from genomic library were found to be polymorphic. These microsatellite markers will be useful resources for population genetic studies of A. assama and other closely related species of saturniids. This is the first report on development of microsatellite markers for any saturniid species

SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation

Microsatellites or SSRs (simple sequence repeats) are ubiquitous short tandem duplications occurring in eukaryotic organisms. These sequences are among the best marker technologies applied in plant genetics and breeding. The abundant genomic, BAC, and EST sequences available in databases allow the survey regarding presence and location of SSR loci. Additional information concerning primer sequences is also the target of plant geneticists and breeders. In this paper, we describe a utility that integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, and PCR simulation against other databases. This simulation allows the performance of global alignments and identity and homology searches between different amplified sequences, that is, amplicons. In order to validate the tool functions, SSR discovery searches were performed in a database containing 28 469 nonredundant rice cDNA sequences