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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. Completed output files can be sent to the GenBank, EMBL, or DDBJ databases by electronic mail.

A Sequin quick guide is available, and describes the format in which your sequences should be saved before importing them into the program. Please review this format before using the Sequin program.

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 or performed a PowerBLAST search within Sequin, the alignments can be displayed as well.

Advantages of Sequin

Sequin automatically performs a number of functions that must be carried out manually in other sequence submissions programs such as BankIt. 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.

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 the CDD Blast function and PubMed searching. Sequin also allows the propagation of features from one sequence in an aligned set to other sequences within the set.