Sentence examples for alignment and annotating from inspiring English sources

Up to now, large and even small amounts of data had to be digested and visualized manually for this task, by writing down all predictions for each sequence, positioning these in the alignment, and annotating a trusted species tree with them.

HMM (hidden Markov models were constructed from alignments of collected proteins generated with MAFFT [ 18] and used to detect homologues in excavates using the HMMer web server search tool [ 19]. Recovered sequences were aligned with MAFFT with sequences from the CDD (conserved domains database) seed alignment and annotated reference sequences.

EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data.

Partial Hirudo protein sequences were extracted from the alignment data and annotated with their corresponding GO categories.

ReXSpecies generates HTML output containing an annotated alignment and an annotated tree as described below.

The resulting multiple alignments were visualized and annotated using the sequence alignment protocol in CLC sequence viewer (CLCBIO, Aarhus, Denmark).

The presence of a direct repeat at the breakpoint, and the overall homology (represented as percent of total number of homologous nucleotides in the alignment), were scored and annotated (Table S1).

Redundancy was removed with cd-hit at a level of maximal 90% sequence identity [ 20], the remaining sequences were aligned with MAFFT (using L-INS-I settings [ 21]) and the resulting multiple alignment was visualized and annotated in Jalview [ 22].

We used the same clustal-generated alignment used for phylogenetic trees and annotated alignments for Prof analysis.

We used BLAT [ 25] alignments of predicted and annotated genes to assess gene prediction accuracy.

This report presents a comprehensive search and scan of NGS genomic alignments to identify and annotate several families of non-protein encoding RNA genes.