The phrase "alignment algorithms and" is correct and usable in written English.
It can be used in contexts discussing computational methods or techniques related to aligning data or structures, often in fields like bioinformatics or machine learning.
Example: "The research focused on alignment algorithms and their effectiveness in processing genomic sequences."
Alternatives: "alignment techniques and" or "alignment methods and".
To identify alternative spliced transcripts for each gene, spidey, a cDNA-to-genomic alignment program, was used to align spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment [ 38].
Repeat regions are problematic for alignment algorithms and users tend to mask sequences before performing the alignments.
These were observed with all applied alignment algorithms and even with relatively high coverage values.
Second, NOTCH1 bears substantial sequence homology to other NOTCH genes, potentially confounding alignment algorithms and generating spurious variant calls.
Finally, future work will explore the possibility of using alternative alignment algorithms and SV predictors in the SHEAR pipeline.
This circumvents the problem of fragmenting genomes into conserved regions, a process that is very sensitive to the parameter settings of alignment algorithms and thus not robust.
For the Sanger dataset, sequences were aligned in Geneious® using the Geneious alignment algorithm and were checked by eye to assure no gaps in protein-coding genes.
Sequences were aligned in ClustalW [ 70] using the pairwise alignment algorithm and alignments were manually controlled and improved locally.
Cloned sequences for each 14-3-3 14-3-3 14-3-3alisoformgainst established gene sequences using a Clustalwereignment alignedhm againstestablishedare (Ibis Biosciences, Carlsbad, CA).
Indel Realign was executed using the full Smith Waterman alignment algorithm and base quality scores of reads were recalibrated in the aligned.BAM files.
