MIGG did sequence retrieval and alignments with ESPript.
In particular, the domain sequence retrieval and multiple sequence alignment tools facilitate the search for conserved residues in the specific domains of selected cryptochromes.
A BioPerl [39] sequence index was built for each subset for sequence and alignment retrieval.
A BioPerl [39] sequence index was built for each data set for sequence and alignment retrieval.
Wrapper scripts were written to streamline protein sequence retrieval, cache alignment results, and enable batch processing of the input.
Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.
The sequence retrieval, alignment, and tree reconstruction were conducted as described elsewhere (Burki et al. 2012) with a few modifications (see supplementary file S2, Supplementary Material online).
The domain-specific mathematical abilities tested were knowledge of symbols, arithmetical fact retrieval, understanding of the positional value of digits, and alignment skills.
The web site provides tools for querying and analysing the data as well as a wide range of documentation, and supports full text and field-based text searches, sequence similarity searching, multiple sequence alignments, batch retrieval and database identifier mapping.
EST-assembly and EST-alignment-based sequence retrieval and prediction resulted in various sequences with atypical start or stop codons indicating that the sequences lack information on the protein C- and N-termini, such as N-terminal organellar targeting signals and C-terminal membrane anchors, or that the ESTs reflect incomplete or wrong splicing or genomic contaminations of the EST libraries.
