Sentence examples for using the local alignment from inspiring English sources

We then aligned the sequences in each cluster using the local alignment algorithm implemented in DIALIGN [ 29], followed by the refinement algorithm from MUSCLE [ 30].

RNaseP and SRP RNAs were identified using a relaxed BLASTN search (Evalue = 0.1) against the Rfam database (Rel 8.0) [156], then searching all hits against respective Rfam models using cmsearch within the INFERNAL covariance model package (v.0.7) using the local alignment option for maximum sensitivity.

These pairs were compared by using the local alignment program water from the EMBOSS package [ 33].

We aligned mature and hairpin sequences of an miRNA to the cultivar-AM560 genome using the local alignment tool BLAST.

BS-Seeker2 using the local alignment mode of Bowtie2 provides an effective way to map these reads.

We computed the sequence similarities between two proteins y and y′ using the local alignment kernel (Saigo et al., 2004).

In addition, we used the local alignment configuration of Bowtie2, which allows reads' end "trimming" to optimize alignment.

To identify significant sequence similarity between distantly related intergenic regions, we used the local alignment algorithm, BlastN, and a profile hidden markov alignment algorithm, HMMER, to search the genome of each species for similarity to each S. cerevisiae intergenic sequence.

Amino acid sequences were originally aligned using the local-alignment algorithm E-INS-I with standard automatic parameters implemented in Mafft v7 [ 32].

To visualize the diversity of N. viridescens precursors, we created a sequence alignment of N. viridescens SPF transcripts using the local-alignment algorithm E-INS-I with automatic parameters implemented in Mafft v7 [ 32] and constructed an Unweighted Pair-Group Method with Arithmethic Averaging (UPGMA) tree in PAUP* [ 33], (Additional file 3).

First, the corresponding Unigenes obtained by keyword searches were aligned with spruce and other plant protein sequences from the public databases using the local TBLASTN alignment tool with an E-value threshold of 1e-5.