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Full-Text Articles in Bioinformatics
Annotation Of Non-Model Species’ Genomes, Taiya Jarva
Annotation Of Non-Model Species’ Genomes, Taiya Jarva
Master's Theses
The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …
Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph, Narjes Sadat Movahedi Tabrizi
Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph, Narjes Sadat Movahedi Tabrizi
Wayne State University Dissertations
Recent progress in DNA amplification techniques, particularly multiple displacement
amplification (MDA), has made it possible to sequence and assemble bacterial
genomes from a single cell. However, the quality of single cell genome assembly has
not yet reached the quality of normal multi-cell genome assembly due to the coverage
bias (including uneven depth of coverage and region blackout) and errors caused by
MDA. Computational methods try to mitigates the amplification bias. In this document
we introduce a de novo co-assembly method using colored de Bruijn graph,
which can overcome the problem of blackout regions due to amplification bias. The
algorithm is …