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The signature peptide was chosen and identified from the tryptic hydrolyzates of bovine lactoferrin by ultra high-performance liquid chromatography and quadrupole-time-of-flight tandem mass spectrometry based on sequence database search.
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Resequencing a key germplasm subset representing various geographically distributed populations can provide scientists with in-depth knowledge of the range of genome variation and genetic diversity within the population based on sequence databases.
Following automatic assignments, annotation of the identified ORFs was performed based on sequence similarity searches against sequence databases and subsequent manual curation and annotation using GenDB 2.4 [ 28].
The sequencing data were analyzed using Basic Local Alignment Search Tool BLASTT 2.3.0) (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and bacterial species were identified based on sequence identity from the database.
tPA derived ESTs were removed based on sequence similarity prior to database searches.
The annotation approach was based on sequence similarity searches in databases.
In contrast to microarrays, RNA sequencing does not require pre-existing genome sequence data from each microbe present, but rather can characterize gene expression based on sequence homology to existing databases.
To develop these assemblies as resources for functional studies, we assigned putative gene names and functional categories [Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)] to assembled transcripts based on sequence comparisons with online databases.
The functional assignment of sequences from captured metagenomes was also carried out in MG-RAST based on sequence similarity matches with different databases along with SEED database where reads were annotated with different subsystems (E-value of 10−5).
The revised annotation was thus based on sequence similarity searches against updated databases, and domain/motif assignment following querying secondary databases (see: Methods).
It may be useful in characterization of orphan receptors and fishing out of homologous sequences from the database, based on sequence similarity.
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