The phrase "a long alignment" is correct and usable in written English.
It can be used in contexts where you are referring to a lengthy arrangement or positioning of items, such as in design, text formatting, or data organization.
Example: "The document required a long alignment of the text to ensure it was properly formatted for presentation."
Alternatives: "an extended alignment" or "a lengthy alignment".
Candidate sequences were determined by a combination of low E value (generally less than E = 0.01) and a long alignment to the HMM model.
Also, the hit had to present continuous cDNA coordinates, i.e., the two exons defining the mouse intron could have a maximum gap of 20 nt in the cDNA, to ensure the intron was not simply a long alignment gap.
Of course, a long alignment is no guarantee for the recovery of the real phylogeny [e.g. [ 125]], since more genes will not necessarily correct biases, the effects of wrong substitution models and class I long-branch effects.
To perform phylogenetic analyses, we produced a long alignment dataset (Aln-1) and two data subsets (Aln-2 and Aln-3) by combining our data with that from Van Bocxlaer et al. and/or van der Meijden et al. [ 2, 3] (Additional file 6).
However, using a long alignment length as a match cut-off with MEGABLAST biases the results towards BLAT and SSAHA2, since FACS do not have an alignment length requirement, while BLAT and SSAHA were unfavoured by using an E-value match cut-off.
As is the case with the BLAST algorithm [ 34], the P-value of a given conserved element varies with the size of the search space, since one is more likely to find a given degree of conservation by random chance in a long alignment than in a short alignment.
To support our findings, we inferred the evolutionary history based on a 706nt long alignment of the 12 reference IAV strains presented in Table 3.
Response: The psaA leader regions have a reliable long alignment, which accents the fact that this promoter considerably differs from the bacterial sigma-70 consensus.
The aligned sequences were inspected, the ends were trimmed to remove sequence missing in any of the 9 genomes, and the alignments of the 12 genes were concatenated to produce a single long alignment.
The authors stress that they used a very long alignment (21,313 bp), that inner nodes got high support values, and that support for a close relationship between myriapods and chelicerates is consistent.
The MSA of these sequences with the consensus sequences of the six maize CR subfamilies and Beetle1 and Beetle2 elements was generated using MEGA5 (Tamura et al. 2011) and manually edited using BIOEDIT (Hall 1999) to remove gaps, and flushed to generate a 2,447-nt 2,447-ntgnment of spanning the RT domain to the polongrine tralignment
