Sequin Getting Started

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 this basic data, Sequin prepares a window containing the initial database record. Many additional forms, which 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 FASTA format format in which your sequences should be prepared before importing into the 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.

Advantages of Sequin
Sequin automatically performs a number of functions which must be carried out manually on other sequence submissions programs such as Authorin and 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.

Sequence Annotation Tools
A number of powerful sequence annotation tools have been integrated into Sequin. The Repeat Finder searches for repeated sequences, such as Alu sequences, in human DNA sequence submissions. The ORF Finder identifies open reading frames within the sequence. Used in conjunction with the Sequence Editor, the ORF Finder can annotate new coding sequences on the record. The Sequence Editor also allows basic editing and translation of nucleotide sequences. If sequences are edited in the Sequence Editor, the sequence locations of the overlapping annotations will be updated as well.

Revised April 24, 1998