Sentence examples for output alignment from inspiring English sources

If a residue in the test sequence was aligned to a non-gap position in the reference alignment, it is correct in the output alignment if it is aligned to that same position, and incorrect otherwise.

In addition, we have a weak anchoring option, where consistent anchor points are only used to constraint the output alignment, but are not necessarily aligned to each other.

Submitted nucleic acid sequences or protein sequences in FASTA format are computed for the output alignment in PHYLIP format using ClustalW; a query initiated in a pre-aligned file in PHYLIP format by other sequence align tools disregards this procedure.

We did not use 'Palindrome' program developed by EMBOSS, since the output did not give the length of sequence and was difficult to make out whether the output alignment is a palindrome or IR sequence.

The output alignment files in SAM format were further processed using SAMtools [ 43].

The default output alignment format is SAM (Sequence Alignment/Map format).

The PHYLIP format output alignments were used to construct distance matrices within each library by using Dnadist from the phylip 3.6 package [33] with the default parameters and using the Jukes-Cantor model [34] option.

The PHYLIP format output alignments were used to construct distance matrices within each library using DNADIST provided in the PHYLIP 3.6 package [49], with default parameters and using the Jukes-Cantor model [50] option.

The output alignments are in bam format [ 82].

This is the main reason why alignment programs may fail to produce biologically reasonable output alignments.

We calculated the average identity (AI) values from automatically generated BLAST output alignments.