Instructions

Please fill in all the fields in the form at the left and then press the SUBMIT button. Your search will be run once each month and will search all new and changed entries in the non-redundant database. Search results will be mailed to the e-mail address you enter at the left. For more details on BLAST searching, see the NCBI BLAST site. Any problems, please contact Bob Gross. Please note that this search is available ONLY for Dartmouth users.


Help

your name: enter your name here (obvious!)

e-mail address for returning results: the results of the search will be sent to this e-mail address twice each month. Please be careful - errors will result in lost e-mail.

DNA sequence name: enter the name you want to use to identify the DNA you will paste in this form.

histogram of scores: if you say yes to this, the results will be returned containing a histogram of scores for the search results.

filtering: This masks out segments of the query sequence that have low compositional complexity, or segments consisting of short-periodicity internal repeats. Keeping filtering on eliminates the return of many database sequences that are not statistically significant.

expect value: the statistical significance threshold for reporting matches against database sequences. The default value of 2 means that 2 matches are expected to be found merely by chance. If the statistical significance of a match is greater than the expect threshold, the match will not be reported. Lower expect thresholds are more stringent, leading to fewer chance matches being reported. The appropriate value will vary with the sequence.

return results as HTML: The BLAST search can return the results to you as plain text or as HTML code. HTML is the language used to specify web pages. Results returned as HTML are suitable to be viewed with a web browser such as Netscape Navigator or Microsoft Internet Explorer. To view HTML results, save the e-mail to a file with the extension ".html" at the end of the file name and use the "Open File" command in the "File" menu of your web browser. Once opened in the browser, you will be able to make links to other sequences to which your sequence is similar.

paste DNA sequence here: This is where the DNA sequence you want to have as your query sequence should go. There are a few rules in order to get this to work correctly. First, remove all spaces, numbers, and any other non-DNA characters from the sequence. The sequence itself cannot have any lines that are longer than 80 characters (BLAST will only use the first 80 characters in a line). The width of the text box is about 60 characters, so if all your sequence lines fit in the box, you are OK. If any sequence lines extend beyond the right edge of the box, you can place the cursor in that sequence line and press RETURN to start a new line. Improperly formatted sequences will lead to unpredictable results.