Replaces accession AW146645
BLAST of Magi repeat database results in statistically defined repeat
BLASTGx yielded no significant hits:
Score E
Sequences producing significant alignments: (Bits) Value
gi|18254412|gb|AAL66753.1|AF464738_4 putative copia-type pol pol 38.9 0.18
BlastN:
Hits a region of the alpha zein gene cluster in between alpha zein 9 and alpha zein 10 [Zea mays]
-
InterPro (nucleotide sequence entered) yielded no useful information:
Restuls of analysis of accession's sequence with repeat masker:
>AW146645 614076B08.y2 614 - root cDNA library from Walbot Lab Zea mays cDNA, mRNA sequence. (633 bp masked -- 100.00% masked) ANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Could not obtain a longer sequence from MADI, MAGI, nor assembled EST's
Repeat blast of the genbank sequence:
>zm_SDRv3.1_5114
Length = 196
Score = 137 bits (69), Expect = 2e-32
Identities = 92/99 (92%), Gaps = 3/99 (3%)
Strand = Plus / Plus
Comput Syst Bioinformatics Conf. 2006;:167-78.
Links
Turning repeats to advantage: scaffolding genomic contigs using LTR retrotransposons.
Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA. ananthk@iastate.edu
The abundance of repeat elements in the maize genome complicates its assembly. Retrotransposons alone are estimated to constitute at least 50% of the genome. In this paper, we introduce a problem called retroscaffolding, which is a new variant of the well known problem of scaffolding that orders and orients a set of assembled contigs in a genome assembly project. The key feature of this new formulation is that it takes advantage of the structural characteristics and abundance of a particular type of retrotransposons called the Long Terminal Repeat (LTR) retrotransposons. This approach is not meant to supplant but rather to complement other scaffolding approaches. The advantages of retroscaffolding are twofold: (i) it allows detection of regions containing LTR retrotransposons within the unfinished portions of a genome and can therefore guide the process of finishing, and (ii) it provides a mechanism to lower sequencing coverage without impacting the quality of the final assembled genic portions. Sequencing and finishing costs dominate the expenditures in whole genome projects, and it is often desired in the interest of saving cost to reduce such efforts spent on repetitive regions of a genome. The retroscaffolding technique provides a viable mechanism to this effect. Results of preliminary studies on maize genomic data validate the utility of our approach. We also report on the on-going development of an algorithmic framework to perform retroscaffolding.
PMID: 17369635 [PubMed - in process]
