BlastnMapping {SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Application.NtMapping}

.NET clr documentation

BlastnMapping

Description

Blastn Mapping for fastaq

BLAST word-size

Length of an exact sequence match, as start region for the final alignment

 blastn -query genes.ffn -subject genome.fna -word_size 11

A BLAST search starts With finding a perfect sequence match Of length given by -word_size. This initial region Of an exact sequence match Is Then extended In both direction allowing gaps And substitutions based On the scoring thresholds.

Changing the initial word-size can help To find more, but less accurate hits; Or To limit the results To almost perfect hits.

• Decreasing the word-size will increase the number Of detected homologous sequences, but hits

can include alignments Of higher fragmentation due To gaps And substitutions (example: search for homologous genes between distant species, see also: -task blastn)

• Increasing the word-size will give less hits As it requires a longer continuous regions Of

exact match. If the word-size Is chosen To be almost the size Of the query, BLAST will search For almost exact matches (example: search for location of gene sequences in the original genome of the gene)

For Short sequences, word-size must be less than half the query length, otherwise reliable hits can be missed.

Default word-sizes

• nucleotide sequence search blastn With Default megablast (bastn): -word_size 28

• nucleotide sequence search blastn only (bastn -task blastn): -word_size 11

• amino acid search (blastp): -word_size 3

Setting the word-size To a very low value (-word_size 5) makes a blastn search very slow.

如果做motif位点搜索，因为motif序列通常比较短，并且有些区域差异很大，所以word size可以设置的比较小

Declare

            
# namespace SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Application.NtMapping
export class BlastnMapping extends Contig {
   AlignmentFullLength: boolean;
   Evalue: double;
   Extensions: list;
   GapsFraction: string;
   # Gaps(%)
   gapsValue: string;
   IdentitiesFraction: string;
   # Identities(%)
   identitiesValue: double;
   # Perfect?
   PerfectAlignment: boolean;
   QueryLeft: integer;
   # Length of BlastnMapping.ReadQuery
   QueryLength: integer;
   QueryRight: integer;
   QueryStrand: Strands;
   # Score(Raw)
   RawScore: integer;
   # The name of the reads query
   ReadQuery: string;
   # The name of the reference genome sequence.
   Reference: string;
   ReferenceLeft: integer;
   ReferenceRight: integer;
   # 在进行装配的时候是以基因组上面的链方向以及位置为基准的
   ReferenceStrand: Strands;
   # Score(bits)
   Score: integer;
   Strand: string;
   # Unique?(这个属性值应该从blastn日志之中导出mapping数据的时候就执行了的)
   Unique: boolean;
}

        

.NET clr type reference tree

1. this class extends from Contig class: Contig
2. use by property member Extensions: list
3. use by property member QueryStrand: Strands
4. use by property member ReferenceStrand: Strands

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