Your aim is therefore to identify sequence variations contained in the DNA sequence for protein
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Practice Problems

Your aim is therefore to identify sequence variations contained in the DNA sequence for protein

Assessment Criteria

Learning Outcomes Tested 1 - 4

Title Should be concise and informative, containing keywords that can be used in information-retrieval systems. Avoid abbreviations and formulae where possible.

Intro LO1.1

Provides adequate but concise literature to explain why the bioinformatics analysis was undertaken.

Intro LO1.2

Explain fundamental bioinformatic principles, including the scope and aims of the bioinformatics analysis.

Method LO2.1

Describes the workflows to identify variations in specific genes or regions of the genome by using in silico analysis of specific sequences by alignment to those in public collections

Method LO4.1

Describes the workflows to patterns of mismatches, which could represent a potential variation.

Method LO4.2

Describes appropriate bioinformatics analyses workflows to map variations to existing records in dbSNP and connect them to functional analyses reported in literature.

Method LO2.2

Justifies the appropriate use of relevant theoretical, mathematical statistical analysis and or Bioconductor statistical packages to probe genomic data.

Method Gen

Overall, provides sufficient detail to allow the experiments and results to be reproduced.

Method Gen

Overall, summarises methods already published and indicated by references to publications where the details may be found: only relevant departures from published methods are described in detail.

Result LO3.1

Reports outcomes from appropriate bioinformatics processes to capture information on variations in specific genes or regions of the genome by using in silico analysis of specific sequences by alignment to those in public collections.

Result LO3.2

Reports the outcomes from analyses to capture information on patterns of mismatches, which could represent a potential variation.

Result LO3.3

Reports outcomes from appropriate bioinformatics analyses to map variations to existing records in dbSNP and connect them to functional analyses reported in literature.

Result LO3.4

Overall, results demonstrate outcomes from appropriate hypothesis driven bioinformatics analyses.

Result Gen

Overall, uses appropriate tables and figures, in-text citations, reference list, appendix materials to support to support the results.

Discuss LO2.3

Critically explains the significance of performing benchmarking studies and describe several of their basic conclusions for MSA and SNP analysis

Discuss LO3.5

Critically discusses the outcomes from SNP analyses and delineate the relevant clinical impacts on phenotypes and or diseases in the context of published work.

Discuss Gen

Overall, provides fluent, logical and accurate description and or reporting of background knowledge, methods, results and discussions.

Assessment Brief

Assessment Title

Assigning functions to SNPs

Learning Outcomes1 and 3

Assessment Task

In assignment A2, you examined the phylogeny and 3D structure of protein P19801-2. Your client has requested for further information about this protein. They have now requested for information on possible variations in the DNA sequence of this protein. Your aim is therefore to identify sequence variations contained in the DNA sequence for protein P19801-2 through BLAST alignment, match it to highly informative records in dbSNP, and connect variations to functional analyses reported in literature to facilitate decision-making processes and enhance the speed and productivity of their research.

Hint
ManagementThe term "variation" refers to both structural and sequence changes. Single nucleotide polymorphisms (SNPs), short sequence insertions and deletions (INDELs), microsatellites (simple sequence repeats), and transposable elements are all types of sequence variations. ...

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