The phrase "a valid alignment" is correct and usable in written English.
It can be used in contexts where you are discussing the correctness or appropriateness of an alignment, such as in mathematics, design, or project management.
Example: "After reviewing the data, we confirmed that the results showed a valid alignment with our initial hypothesis."
Alternatives: "an acceptable alignment" or "a correct alignment".
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.
These two fixed genes guarantee generating a valid chromosome, and therefore a valid alignment.
There are two restrictions on each RB to make a valid alignment, they are as follows: 1.
We used the −k = 1 option in BowTie2, which reports a single valid alignment for each read in the library.
Next the reads were aligned against the HOX cluster allowing for no mismatches, all valid alignments for each read were reported.
Since the first release of the program DIALIGN in 1996, a 'direct' greedy approach has been used where local pairwise alignments (fragments) are checked for consistency one-by-one to see if they can be included into a valid multiple alignment.
A valid overlap alignment is an ordered set of matches M1, M2,…, M w that allows experimental maps and in silico maps to only partially align with each other, with M1 and M w each corresponding to an end of one of the maps (for example, Fig. 1 e).
A valid glocal alignment is an ordered set of matches M1, M2,…, M w between experimental and in silico fragments, such that all the experimental fragments o1, o2,…, o m are aligned to a subset of the in silico fragments r t, r t +1,…, r v, and both sets are orderly partitioned by all the matches M1… w without overlaps, with w≤ m and w≤ v− t+1.
