SUBMISSION AND RETRIEVAL OF AN ALIGNED SET OF NUCLEIC ACID SEQUENCES

Abstract

An important part of many studies published in the Journal of Phycology is the construction and analysis of an alignment of related nucleotide sequences. These alignments are valuable to other investigators, especially when the data provide a basis for more than one possible alignment. Publication of alignments, however, is prohibitively expensive, and the data are difficult to retrieve and use in this form. Several electronic archives for these alignments now exist, and information is provided here on the submission and retrieval of alignments at the National Center for Biotechnology Information (NCBI), the European Bioinformatics’ Institute (EBI), and TreeBASE. Emphasis is placed on the use of Sequin and Entrez at the NCBI, because these programs have been modified recently and they provide a fluid and integrated system to submit and retrieve sequence and alignment records and related information. Other useful features of Entrez (e.g. free Medline searches) are noted.