The phrase "alignment to genes" is correct and usable in written English.
It can be used in contexts related to genetics, biology, or bioinformatics, particularly when discussing how certain factors or elements correspond or relate to genes.
Example: "The study focused on the alignment to genes in order to understand the genetic variations among different populations."
Alternatives: "correspondence with genes" or "relation to genes".
Assembled unigenes were annotated in multiple public databases based on similarity alignments to genes and proteins.
The miRNA tissue-specific pools sequenced for the tammar were used as an analog to the miRBase sequences and counts of alignments to genes were generated using the short read alignment tool Bowtie (see methods).
Although the methods used by these various genome and transcriptome annotation projects differ, they typically include sequence alignments to genes and transcript sequences from other species, protein domain identification, gene ontology (GO) assignments (18), gene family computations and functional descriptions.
The related microarray data of Eads et al. and Shaw et al. in companion papers demonstrate that most of the sequenced Daphnia genes are differentially transcribed in a manner consistent with their putative functions, thus reinforcing their provisional annotations based on sequence alignments to genes from model insects.
The overall pattern of MSLL end read alignments to genes (Fig. 1) was as expected, with 5' and 3' peaks and a central minimum reflecting the relationship of MSLL ends to epigenetic boundaries, and with both of these characteristics more pronounced for the HpaII clones relative to the SalI clones.
Only the two most significant alignments were retained in an attempt to avoid spurious alignment to multiple genes from different stickleback linkage groups (for example due to similarity of genes from the same gene family).
The tRNA genes were annotated using tRNAscan-SE 1.3.1 [ 26] and rRNA genes identified with RNAmmer 1.2 [ 27] and alignment to corresponding genes of HAMBI 540T and HAMBI 1141.
The chimeric RNAs showed partial alignment to two genes, which often are present on different chromosomes.
Increased alignment to annotated genes improves the robustness of RNA-seq results, thus we selected the Ensembl-UMD3.1 annotation for further analysis.
Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes.
