Name
Title | ||
|---|---|---|
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. |
Abstract | ||
|---|---|---|
Genomic sequences are highly redundant and contain many types of repetitive DNA. Fuzzy tandem repeats (FTRs) are of particular interest. They are found in regulatory regions of eukaryotic genes and are reported to interact with transcription factors. However, accurate assessment of FTR occurrences in different genome segments requires specific algorithm for efficient FTR identification and classification.We have obtained formulas for P-values of FTR occurrence and developed an FTR identification algorithm implemented in TandemSWAN software. Using TandemSWAN we compared the structure and the occurrence of FTRs with short period length (up to 24 bp) in coding and non-coding regions including UTRs, heterochromatic, intergenic and enhancer sequences of Drosophila melanogaster and Drosophila pseudoobscura. Tandems with period three and its multiples were found in coding segments, whereas FTRs with periods multiple of six are overrepresented in all non-coding segment. Periods equal to 5-7 and 11-14 were characteristic of the enhancer regions and other non-coding regions close to genes.TandemSWAN web page, stand-alone version and documentation can be found at http://bioinform.genetika.ru/projects/swan/www/Supplementary data are available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2006 | 10.1093/bioinformatics/btk032 | Bioinformatics |
Keywords | Field | DocType |
genomic sequence,tandemswan software,drosophila pseudoobscura,classification. results: we have obtained formulas for p-values of ftr occurrence and developed an ftr identification algorithm implemented in tandemswansoftware.usingtandemswanwecomparedthestruc- ture and the occurrence of ftrs with short period length up to 24 bp in coding and non-coding regions including utrs,non-coding region,gene expression,tandemswan web page,ftr occurrence,non-coding segment,efficient ftr identification,short fuzzy tandem,coding segment,heterochromatic,possible role,ftr identification algorithm,whereas,intergenic and enhancer sequences of drosophila melanogaster and drosophilapseudoobscura.tandemswithperiodthreeanditsmultiples were found in coding segments,drosophila melanogaster,genome sequence,tandem repeat,regulation of gene expression,transcription factor,repetitive dna | Genome,Sequence alignment,Drosophila pseudoobscura,Tandem repeat,Repeated sequence,Gene,Biology,Intergenic region,Bioinformatics,Enhancer | Journal |
Volume | Issue | ISSN |
22 | 6 | 1367-4803 |
Citations | PageRank | References |
30 | 1.94 | 6 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Valentina Boeva | 1 | 172 | 14.86 |
| Mireille Regnier | 2 | 51 | 9.56 |
| Dmitri Papatsenko | 3 | 75 | 5.78 |
| Vsevolod Makeev | 4 | 90 | 9.70 |