|Getting Started with Sequin|
Overview of Sequin
General information about the submitters and the sequence is entered into Sequin on a pair of introductory forms. The user is prompted to import the nucleotide and any associated amino acid sequences into the program in FASTA format. From these basic data, Sequin prepares a window containing the initial database record. Many additional forms, that provide space for adding new or modifying existing annotations, are accessible from this window. Sequin also contains a built-in validation tool which checks the record for accuracy and consistency and suggests solutions for many problems.
Displaying the Record
Sequin can display the initial record in a number of different formats. The record can be seen as it would appear in the GenBank, EMBL, or DDBJ databases. Sequences and certain annotations can also be viewed in a graphical format, permitting, for example, a schematic display of the locations of mRNAs and coding sequences along a genomic DNA sequence. If you have submitted a set of aligned sequences, the alignments can be displayed as well.
Advantages of Sequin
Sequin automatically performs a number of functions necessary for submission. For example, Sequin obtains the proper genetic code from the name of the organism and automatically determines coding region intervals on the nucleotide sequence by back-translation of the protein sequence. Researchers who submit large numbers of related sequences can make use of the fact that Sequin can also interpret the name of the organism, strain, and other biological source information directly from a line of data entered along with each nucleotide sequence. Sequin also allows the designation of groups of sequences as population, phylogentic, mutant, or environmental sets for display in the PopSet division of Entrez and the propagation of annotation from one member of the set to all others through an alignment.
Sequence Annotation Tools
A number of powerful sequence annotation tools have been integrated into Sequin. The ORF Finder identifies open reading frames within the sequence. The Sequence Editor allows basic editing and translation of nucleotide sequences. With the Update Sequence function, Sequin can import and align a replacement or overlapping sequence to the sequence in the record and propagate features between the two aligned sequences. In Network-Aware mode, Sequin integrates PubMed searching. Sequin also allows the propagation of features from one sequence in an aligned set to other sequences within the set.
Questions or Comments?
Revised April 20, 2011.