A new method for designing degenerate primers and its use in the identification of sequences in Brachiaria showing similarity to apomixis-associated genes

نویسندگان

  • Eduardo Gorrón
  • Fausto Rodríguez
  • Diana Bernal
  • Luis Miguel Rodriguez-Rojas
  • Adriana Bernal
  • Silvia Restrepo
  • Joe Tohme
چکیده

MOTIVATION We developed a technique and a tool for degenerate primer design based on multiple local alignments employing the MEME algorithm supported with electronic PCR. The objective is to find adequate primers starting from sequences with poor global similarity. We show an example of its application in our laboratory to find sequences in Brachiaria with similarity to ESTs related to apomixis.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Designing Of Degenerate Primers-Based Polymerase Chain Reaction (PCR) For Amplification Of WD40 Repeat-Containing Proteins Using Local Allignment Search Method

Degenerate primers-based polymerase chain reaction (PCR) are commonly used for isolation of unidentified gene sequences in related organisms. For designing the degenerate primers, we propose the use of local alignment search method for searching the conserved regions long enough to design an acceptable primer pair. To test this method, a WD40 repeat-containing domain protein from Beauveria bass...

متن کامل

Identification and characterization of a NBS–LRR class resistance gene analog in Pistacia atlantica subsp. Kurdica

P. atlantica subsp. Kurdica, with the local name of Baneh, is a wild medicinal plant which grows in Kurdistan, Iran.  The identification of resistance gene analogs holds great promise for the development of resistant cultivars. A PCR approach with degenerate primers designed according to conserved NBS-LRR (nucleotide binding site-leucine rich repeat) regions of known disease-resistance (R) gene...

متن کامل

DNA Fingerprinting Based on Repetitive Sequences of Iranian Indigenous Lactobacilli Species by (GTG)5- REP-PCR

Background and Objective: The use of lactobacilli as probiotics requires the application of accurate and reliable methods for the detection and identification of bacteria at the strain level. Repetitive sequence-based polymerase chain reaction (rep-PCR), a DNA fingerprinting technique, has been successfully used as a powerful molecular typing method to determine taxonomic and phylogenetic relat...

متن کامل

Molecular Detection of Novel Genetic Variants Associated to Anaplasma ovis among Dromedary Camels in Iran

To the best of our knowledge, little information is available regarding the presence of Anaplasma species in camels in Iran. This study sought to investigate the presence of Anaplasma species by microscopy and polymerase chain reaction (PCR) assays in 100 healthy dromedaries (Camelus dromedarius) arriving for slaughter. The microscopic examination of Giemsa-stained blood films revealed that Ana...

متن کامل

Phylogeny and genetic diversity of Fusarium graminearum species complex associated with Fusarium head blight of wheat in Moghan plain (Iran)

Thirty-seven isolates of Fusarium graminearum species complexobtained from wheat heads with Fusarium head blight symptoms were selected and used for phylogenetic studies. They were collected from different localities of Moghan plain (Ardebil province, Iran). Partial sequences of translation elongation factor 1-alpha (TEF), putative reductase (RED) and UTP-ammonia ligase (URA) genes were amplifi...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Bioinformatics

دوره 26 16  شماره 

صفحات  -

تاریخ انتشار 2010