Phaseolus coccineus DFCI Gene Index (version 1)

Overview
2009
  • Preparation of EST data: Sequences were extracted from dbEST and were subjected to quality control screening (vector, E. coli, polyA, T, or CT removal, minimum length = 100 bp, < 3% N).
  • Preparation of transcript (ET) database: All sequences from the appropriate divisions of GenBank (including RefSeq) were extracted. Non-coding sequences were discarded and cDNAs and coding sequences from genomic entries were saved. Sequences and related information (e.g. PubMed links) are stored in the qcGene database (qcGene).
  • Assembly: Cleaned EST sequences and non-redundant transcript (ET) sequences were combined. Using the Paracel Transcript Assembler Program, sequences were assembled into contigs. TCs are consensus sequences based on two or more ESTs (and possibly an ET) that overlap for at least 40 bases with at least 94% sequence identity. These strict criteria help minimize the creation of chimeric contigs. These contigs are assigned a TC (Tentative Consensus) number. TCs may comprise ESTs derived from different tissues. The best hits for TC's were assigned by searching the TC set against a non-redundant amino acid database(nraa) using BLAT. The top five hits based on score were selected and displayed for each TC.
  • Caveats: TCs are only as good as the ESTs underlying them; there may be unspliced or chimeric ESTs and thus TCs. There is still redundancy in the TC set because sequences must match end to end and at a certain percent identity to be combined. Directionality of the TCs should not be assumed. Not all TCs contain protein-coding regions.
Properties
Additional information about this project:
Property NameValue
TypeResearch Experiment
Research Area
Breeding & Genetics

Plant breeding is the art and science of changing the traits of plants in order to produce desired characteristics. Plant breeding can be accomplished through many different techniques ranging from simply selecting plants with desirable characteristics for propagation, to more complex molecular techniques. ... [more]

 
Related Species

Phaseolus coccineus, known as runner bean, scarlet runner bean, or multiflora bean, is a plant in the Fabaceae family. Runner beans have also been called "Oregon Lima Bean", and in Nahuatl "ayocotl" or in Spanish "ayocote". It differs from the common bean (P. vulgaris) in several respects: the cotyledons stay in the ground during germination, and the plant is a perennial vine with tuberous roots (though it is usually treated as an annual). This species originated from the mountains of Central America. Most varieties have red flowers and multicolored seeds (though some have white flowers and white seeds), and they are often grown as ornamental plants. ... [more]

 
Sequences, Variants & Markers
Data Type Number of Sequences Number of Variants Number of Markers
contig 72,929*