The key differences between these tools and Hammock are (i) Hammock starts the iterative procedure from multiple clusters, so it performs multiple database (the sequence pool) searches in parallel; (ii) Hammock starts the iterative procedure from clusters of sequences, not from a single sequence and (iii) Hammock performs the merging step.
DNA sequencing of the 353 pb fragment followed by multiple alignment with database sequences for Leishmania species indicated Le. infantum, the etiological agent of VL, as the infecting agent in both pool samples of Lu. longipalpis.
We designed amplification primers based on conserved sequences in the multiple alignments of database sequences retrieved from the genomes of Homo sapiens, Pan troglodytes, Gorilla gorilla, Pongo pygmaeus, Macaca mulatta, and Papio hamadryas.
To ensure that no additional related genes were overlooked by the database search, the identified BrIPT and BrCKX genes were used as query sequences in additional multiple database searches to confirm the initial list of genes.
We inferred multiple orthologous relationships between ab initio predicted products with database sequences (excluding mouse database orthologs).
A total of 1,695 X. dendrorhous ORFs were identified through comparison with sequences in multiple databases, and the intron-exon structures of these sequences were determined.
When multiple contigs/singletons match the same database sequence, LANE runner 2.0 performs Clustal Omega (Sievers and Higgins 2014) alignments to define the relative positions of the input sequences and assembles them into a "one-to-many consensus".
Sequences were annotated by sequence similarity to multiple databases, yielding the above number of annotations.
To perform a multiple sequence alignment, sequences homologous to human SEC23B were assembled in a multiple sequence alignment using database UniProtKB release 15.0 of March 25, 2009; program NCBI BLASTP 2.0.12 on http://services.uniprot.org (http://services.uniprot.org/blast/).org/blast/
Comparative analyses were performed with cluster sequences as queries versus multiple databases including C. elegans Wormpep v.203 protein database [ 46].
