BlastnMapping

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