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The upper DNA molecule differs from the lower DNA molecule at a single base-pair location (a G/A polymorphism) In genetics and bioinformatics, a single-nucleotide polymorphism (SNP / s n ɪ p /; plural SNPs / s n ɪ p s /) is a germline substitution of a single nucleotide at a specific position in the genome.
The use of SNPs is being extended in the HapMap project, which aims to provide the minimal set of SNPs needed to genotype the human genome. SNPs can also provide a genetic fingerprint for use in identity testing. [1] The increase of interest in SNPs has been reflected by the furious development of a diverse range of SNP genotyping methods.
A SNP array can also be used to generate a virtual karyotype using software to determine the copy number of each SNP on the array and then align the SNPs in chromosomal order. [10] SNPs can also be used to study genetic abnormalities in cancer. For example, SNP arrays can be used to study loss of heterozygosity (LOH). LOH occurs when one allele ...
Single nucleotide polymorphism annotation (SNP annotation) is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query.
The calculation of prior probabilities depends on available data from the genome being studied, and the type of analysis being performed. For studies where good reference data containing frequencies of known mutations is available (for example, in studying human genome data), these known frequencies of genotypes in the population can be used to estimate priors.
Nucleotide sequence analyses identify functional elements like protein binding sites, uncover genetic variations like SNPs, study gene expression patterns, and understand the genetic basis of traits. It helps to understand mechanisms that contribute to processes like replication and transcription. Some of the tasks involved are outlined below.
Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP/indel calling and alignment.
High sensitivity and specificity, using base qualities at all steps in the alignment. Includes adapter trimming, base quality calibration, Bi-Seq alignment, and options for reporting multiple alignments per read. Use of ambiguous IUPAC codes in reference for common SNPs can improve SNP recall and remove allelic bias. Yes Yes Yes
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