Sentence examples for valid alignment from inspiring English sources

A valid alignment satisfies the following criteria: 1) the similarity between aligned region is ≥ mi n s, 2) the length of the aligned region is ≥ mi n ol, and 3) the overhang of the alignment is ≤ ma x oh.

Bowtie was implemented in the –v alignment mode with the maximum number of mismatches set to 3. Paired end reads were aligned to the transcriptome with both read pairs needing a valid alignment within a given locus to be counted as a match.

Default alignment policies of bowtie were enforced: a valid alignment could have a maximum of two mismatches and if a read aligned equally well to multiple places in the genome, one was chosen at random.

Default alignment policies of Maq were enforced: a valid alignment could have a maximum of two mismatches and if a read aligned equally well to multiple places in the genome, one was chosen at random.

Each valid alignment configuration was converted to genomic nucleotide positions since the chromosomal locations of the open reading frames were known.

These two fixed genes guarantee generating a valid chromosome, and therefore a valid alignment.

A similar number of reads from CAST yield nearly twice as many valid alignments, and relaxing the aligner settings does not correct this problem (data not shown).

Of the additional 1,520 read-pairs with valid alignments in which one or both reads aligned to more than one contig, for 82% (1,239) there was at least one contig to which both reads aligned with opposite orientations.

Next the reads were aligned against the HOX cluster allowing for no mismatches, all valid alignments for each read were reported.

Only hits above both thresholds are considered as valid alignments in the following evaluation.

All valid alignments per read were reported allowing up to three mismatches.