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| Go to CyanoBase (http://www.kazusa.or.jp/cyano/) | CyanoBase is a site that facilitates retrieval of cyanobacterial sequence information from the Kazusa DNA Research Institute database |
| Click on Anabaena sp. PCC 7120 | Anabaena sp. PCC 7120 is also known as Nostoc. When you get to the page, note that Anabaena has seven replicons: one large chromosome and six plasmids (alpha through zeta). |
| Click on Similarity Search | This brings you to a local implementation of BLAST, a program designed to find similarities to a given sequence in a genome or in a set of proteins or genes. |
| Click on Overall DNA sequences/BLASTN | There many flavors of BLAST, depending on what kind of sequence you have (DNA or protein) and what you want to compare it against (DNA or protein). BLASTN compares a small DNA query against a large DNA database. |
| Change Number of sequences for which alignments will be reported to 50. | The program runs quick, so if you decide later you want more than 50 similar sequences reported, it's not a big deal to rerun the search. |
| Paste in your sequence. | The sequence may be in FastA format or pure sequence. Upper case/lower case doesn't matter, nor does spaces or numbers. |
| Click the Submit Query button. | You should get output in a few seconds. |
| Scroll down until you see lines
beginning:
Query: Subjct: |
In BLAST searches of large databases (i.e. of GenBank), the graphical display and the list of sequences producing the best alignments are very informative. Not here, where the database covers just a single organism. The line reporting a hit in the chromosome obscures the fact that there may be multiple hits. |
| Examine hits (each beginning with Query:) | The Query is the sequence you provided. The Subjct is the sequence in the database (the coordinates of the sequence are reported). This implementation of BLAST is hard-wired to let pass only those hits with an E-value (expectation) of 10 or better. In brief, the smaller the E-value, the closer the hit is to the query. |
| Congratulate self | You're done! |