Sentence examples for minimum seed length from inspiring English sources

Default settings were used within the program, with parameters including end-to-end mode, a minimum seed length of 22 nt, and a mismatch penalty of 6.

Besides the length k, two other important parameters are the minimum seed length w(≥ k) and the stride s used to move through the database.

It allows the processing of next-generation RNA-seq data by permitting the user to specify different parameters to align sequence reads to a genome, such as number of mismatches allowed, orientation of mate-pair reads, and minimum seed length.

After the filtering step, clean reads were mapped to the horse reference genome (Ensembl EquCab2.0, release 72) [ 1] with BWA version 0.7.5a [ 61] with minimum seed length (-k 15) and Mark shorter split hits as secondary (-M).

The sequencing reads were mapped to the Arabidopsis genome (TAIR10; http://www.arabidopsis.org) using Bowtie with the following mapping parameters: the quality matrix, phred64-quals; the minimum seed length, l = 20; the allowed mismatch in the seed, n = 1 [ 28].

The non-ribosomal RNA fragments were mapped against the 382 reference genomes of the HMP gastrointestinal tract database using bwa v. 0.7.5 (−k 19 option for minimum seed length) [ 13] and SAMtools [ 33] for storing and filtering nucleotide sequence alignments.

Minimum Seed Read Length was chosen to get two coverages between 12 and 25×.

The following settings were used: mismatched SSR-search with a fixed mismatch penalty; minimum score: 15; fixed mismatch penalty: 5; minimum SSR-seed length: 8; minimum SSR-seed repeats: 3; max mismatches at once: 5; If not denoted otherwise, a d max (maximum distance between adjacent microsatellites as to account as compounded) of 10 bp was used.

The assembly was done with gsAssembler (Newbler v2.7, Roche Diagnostics Corporation, Basel, Switzerland) by considering the default parameters, including a minimum read length: 20; seed length: 16; seed step: 12; minimum overlap length: 40 and minimum overlap identity: 90.

The assembly parameters used were seed step 12, minimum overlap 40, minimum overlap identity 95% and seed length 16, with default quality filter, adapter and primer trimming of the input reads.

The hybrid assembly with both 454 and Illumina data included three major steps: First, 454 reads alone was pre-assembled by Newbler with seed length 16, minimum overlap length 40 and minimum overlap identity 95%; second, Illumina reads were pre-assembled alone using Velvet with K-value 29.