The phrase "alignments is required" is not correct in written English.
It should be "alignment is required" to be grammatically accurate.
Example: "In order to proceed with the project, alignment is required between all team members on the objectives."
Alternatives: "alignment is necessary" or "alignment is essential."
Given the high degree of sequence similarity between some of the stefin members (Figure 2A), gene sequence alignments were required to design SYBR green-based qRT-PCR assays specific to Stfa1 (detecting also BC117090 and BC100530), Stfa2, Stfa2l1, and Stfa3 (Text S1 and Table S3).
To be considered, BLAST alignments were required to be unique in the genome.
Better strategies for dealing with reads with multiple alignments are required.
Alignments were required to have 95% sequence identity, 95% coverage, and no insertions or deletions.
All alignments were required to include at least 150 amino acids.
The alignments were required to be paired, with stringent filtering applied to reduce false-positive alignments from the dataset (see Methods).
Single-exon alignments were required to include at least 50 bp, while in multi-exon alignments, each aligned exon was required to be longer than 10 bp, with introns between 5 bp to 5000 bp.
In the case of PconsC, to achieve maximum performance a set of eight different alignments are required, from two different alignment methods and four parameters settings in each case.
Gene-EST alignments were required to show at least a 90% identity across 100 bp to be recorded as a match and the number of BLASTN hits were used as a proxy for expression levels.
When manual curation of taxa or alignments was required, additional trees were built using RAxML rapid bootstrapping (100 replications) and maximum-likelihood (ML) search assuming a WAG amino acid model of substitution and Γ site heterogeneity model (Stamatakis 2006).
