Sequence

Functionalities regarding genomic sequence analysis.

Finds genomic features overlapping genomic positions, like exons, reconstructs offsets into transcripts, and computes the amino-acid changaes of variants. Additionally finds mutations in exon junctions, and genes with high frequencies of mutations.

Tasks

Positions, ranges, and mutations are specified using a common format. Each is identified by several fields separated by the character :. Positions are represented as chromosome:position i.e. 12:4234412. Mutations have an additional field representing the mutant allele chromosome:position:allele i.e. 12:4234412:T (the reference allele is redundant, as it is specified by the chromosome and position). Indels are represented as in the following examples: +A or +ATC for one and three base insertions repectively or - and --- for one or three deletions repectively. Chromosome ranges are specified as chromosome:start:end as in 12:4234412:4244412.

It supports multiple organisms. The format of the organism input is the organism short code (Hsa for Homo sapiens, or Mmu for Mus musculus) optionally followed by the date of the build. For example, Hsa/jan2013 for a recent build or Hsa/may2009 for the hg18 build.

The watson input is used to specify if the variants are described in reference to the watson or forward strand, or in reference to the strand that holds the overlapping gene. Using the wrong convention may make some mutations coincide with the reference. The is_watson method can take a guess by checking this criteria.

Specifying the vcf parameter will interpret the input as a VCF file, and will run the genomic_mutations task to extract the mutations from it

The main tasks are: mutated_isoforms_fast, splicing_mutations, and affected_genes

• TSS
• TSS_in_range
• add_reference Add reference to mutations as (ref\>mut)
• affected_genes Finds genes affeted by genomic mutations, either by amino-acid changes on their protein products, or by changes in splicing sequences
• binomial_significance_syn For a list of mutations, find genes that suffer a higher rate of mutation than expected. Considers also synonymous mutations
• exon_junctions Report exon junctions overlapping positions
• exons Report exons overlapping positions
• expanded_vcf Expands the `INFO` and `FORMAT/Sample` fields of VCF files in to a standard TSV format
• gene_strand_reference Report the reference base at the provided positions on the gene coding strand
• genes Report genes overlapping positions
• genes_at_ranges Report genes overlapping ranges
• genomic_mutations Extract genomic mutations from a VCF file that match a quality criteria
• is_watson Guess wether the mutations provided are given in the watson strand or the gene strand
• mutated_isoforms Computes the consequence of genomic mutations in terms of amino-acid changes in protein isoforms
• mutated_isoforms_fast One-step implementation of the `mutated_isoforms` task
• reference Report the reference base at the provided positions
• sequence_ontology
• splicing_mutations Find mutations that may affect the splicing of protein coding transcripts
• to_watson
• transcript_offsets Computes the offset inside the coding sequence of the transcripts overlapped the genomic mutations that overlap them.
• transcripts Report transcripts overlapping positions
• type Report the type of base change: transition, transversion, indel, unknown or none at all