sequence analysis
Dotaz
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elektronický časopis
- Konspekt
- Obecná genetika. Obecná cytogenetika. Evoluce
- NLK Obory
- biologie
- genetika, lékařská genetika
- NLK Publikační typ
- elektronické časopisy
- MeSH
- aminokyseliny MeSH
- DNA virů analýza MeSH
- geny MeSH
- nukleotidy MeSH
- onkogenní viry MeSH
- RNA virová MeSH
- skot MeSH
- zvířata MeSH
- Check Tag
- skot MeSH
- zvířata MeSH
- Publikační typ
- srovnávací studie MeSH
... and Overview, 1 Prediction of RNA Secondary Structure, 327 -- Chapter 2 -- Collecting and Storing Sequences ... ... in the Laboratory, 29 -- Chapter 3 -- Alignment of Pairs of Sequences, 65 Chapter 4 -- Introduction ... ... to Probability and Statistical Analysis of Sequence Alignments, 121 -- Chapter 5 -- Multiple Sequence ... ... Alignment, 163 Charter 6 -- Sequence Database Searching for Similar Sequences, 227 -- Chapter 7 -- Phylogenetic ... ... -- Chapter 1 2 -- Bioinformatics Programming Using Perl and Perl Modules, 549 -- Chapter 1 3 -- Analysis ...
2nd ed. xii, 692 s. : il.
- MeSH
- biologické vědy MeSH
- genetika MeSH
- Konspekt
- Obecná genetika. Obecná cytogenetika. Evoluce
- NLK Obory
- genetika, lékařská genetika
UWBC biotechnical resource series
XV, 279 s. : il. ; 24 cm
1 online zdroj
- MeSH
- mitochondriální DNA * MeSH
- sekvenční analýza DNA MeSH
- Publikační typ
- periodika MeSH
- Konspekt
- Biochemie. Molekulární biologie. Biofyzika
- NLK Obory
- genetika, lékařská genetika
RepeatExplorer2 is a novel version of a computational pipeline that uses graph-based clustering of next-generation sequencing reads for characterization of repetitive DNA in eukaryotes. The clustering algorithm facilitates repeat identification in any genome by using relatively small quantities of short sequence reads, and additional tools within the pipeline perform automatic annotation and quantification of the identified repeats. The pipeline is integrated into the Galaxy platform, which provides a user-friendly web interface for script execution and documentation of the results. Compared to the original version of the pipeline, RepeatExplorer2 provides automated annotation of transposable elements, identification of tandem repeats and enhanced visualization of analysis results. Here, we present an overview of the RepeatExplorer2 workflow and provide procedures for its application to (i) de novo repeat identification in a single species, (ii) comparative repeat analysis in a set of species, (iii) development of satellite DNA probes for cytogenetic experiments and (iv) identification of centromeric repeats based on ChIP-seq data. Each procedure takes approximately 2 d to complete. RepeatExplorer2 is available at https://repeatexplorer-elixir.cerit-sc.cz .
- MeSH
- DNA sondy chemie genetika MeSH
- DNA chemie genetika MeSH
- genomika metody MeSH
- lidé MeSH
- repetitivní sekvence nukleových kyselin MeSH
- sekvenční analýza DNA metody MeSH
- shluková analýza MeSH
- software MeSH
- transpozibilní elementy DNA MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
MOTIVATION: Satellite DNA makes up significant portion of many eukaryotic genomes, yet it is relatively poorly characterized even in extensively sequenced species. This is, in part, due to methodological limitations of traditional methods of satellite repeat analysis, which are based on multiple alignments of monomer sequences. Therefore, we employed an alternative, alignment-free, approach utilizing k-mer frequency statistics, which is in principle more suitable for analyzing large sets of satellite repeat data, including sequence reads from next generation sequencing technologies. RESULTS: k-mer frequency spectra were determined for two sets of rice centromeric satellite CentO sequences, including 454 reads from ChIP-sequencing of CENH3-bound DNA (7.6 Mb) and the whole genome Sanger sequencing reads (5.8 Mb). k-mer frequencies were used to identify the most conserved sequence regions and to reconstruct consensus sequences of complete monomers. Reconstructed consensus sequences as well as the assessment of overall divergence of k-mer spectra revealed high similarity of the two datasets, suggesting that CentO sequences associated with functional centromeres (CENH3-bound) do not significantly differ from the total population of CentO, which includes both centromeric and pericentromeric repeat arrays. On the other hand, considerable differences were revealed when these methods were used for comparison of CentO populations between individual chromosomes of the rice genome assembly, demonstrating preferential sequence homogenization of the clusters within the same chromosome. k-mer frequencies were also successfully used to identify and characterize smRNAs derived from CentO repeats.
- MeSH
- centromera genetika MeSH
- chromozomy rostlin genetika MeSH
- DNA rostlinná genetika MeSH
- konzervovaná sekvence genetika MeSH
- molekulární sekvence - údaje MeSH
- rýže (rod) genetika MeSH
- satelitní DNA genetika MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
