Sentence examples for multiple sequence databases from inspiring English sources
Many sequences were represented multiple times with varying identifiers as our custom database was generated by pooling multiple sequence databases together.
Predicted proteins were functionally annotated based on match against multiple sequence databases, including Swissprot, COG, Pfam and nr databases using an e-value threshold of 1e-5 for both BLASTp and HMMer searches.
With the exception of poorly documented or mis-documented catfish species in GenBank and BOLD databases, multiple sequence alignments between consensus sequences (generated from this study) and consensus sequences from the two databases showed high identities (Figure 2).
Thus it is possible to retrieve a multiple sequence alignment from the database, edit it manually and write it back to the database.
Once sequences were collected in the database, multiple sequence alignments were generated with ClustalW [22].
Through hidden Markov models and multiple sequence alignments, the Pfam database collects domain information for a large quantity of protein families.
To confirm the identity of the ROCO domains of these Entamoeba sequences we performed iterative multiple sequence alignments, HMM construction, database searches and realignment, to assemble the data presented as Figure 4.
A small number of existing databases collects multiple sequence alignment of protein sequences that share a proved (experimentally) or predicted (from sequence similarity) function.
The ITS sequences were aligned to each other as well as the sequences retrieved from the NCBI databases, using multiple sequence alignment software CLUSTAL W program with default settings [ 19].
If a strain had multiple sequences in the databases, we preferentially kept the IRD sequence and preferentially kept the longest sequence in IRD.
For each individual protein in the complex, we constructed multiple sequence alignments by querying the UniProt sequence database (Wu et al., 2006) for homologous sequences.
