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It takes in and returns fastq or fasta formatted sequence files. ShortRead is a package provided in the R (programming language) / BioConductor environments and allows input, manipulation, quality assessment and output of next-generation sequencing data. This tool makes possible manipulation of data, such as filter solutions to remove reads ...
Biological sequence formats are a collection of file formats that are used in the biomedical sciences. There are a number of these. Most of these formats were developed for use in particular programmes and have subsequently been reused by other programmes. A number of web sites are available which will convert one of these formats to another.
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.
Functional genomics uses mostly multiplex techniques to measure the abundance of many or all gene products such as mRNAs or proteins within a biological sample. A more focused functional genomics approach might test the function of all variants of one gene and quantify the effects of mutants by using sequencing as a readout of activity.
Slider is an application for the Illumina Sequence Analyzer output that uses the "probability" files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Yes Yes No No [53] [54] 2009-2010 SOAP, SOAP2, SOAP3, SOAP3-dp SOAP: robust with a small (1-3) number of gaps and mismatches.
The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs. This format was developed during the Human Genome Project [1] and then adopted by other sequencing
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The EMBL Nucleotide Sequence Database uses a flat file plaintext format to represent and store data which is typically referred to as EMBL-Bank format. [20] EMBL-Bank format uses a different syntax to the records in DDBJ and GenBank, though each format uses certain standardised nomenclature, such as taxonomies as defined by the NCBI Taxon database.