Input types for Tracker
Input can be given to Tracker in two formats:
  • Fasta formatted sequencs
  • ENSEBL Gene IDs
The program is informed about what input type to use by selecting the correct radio button below the input textboxes.

One or two clusters
Mainly it's convenient to give sequences as one cluster. In some cases it is however practical to give sequences as two different clusters. This happen e.g. when you have results from two separate sample sets that you wish to compare. The decision whether to give your sequences as one or two clusters is made by selecting the correct option from the radio buttons below the sequence input boxes.

Search patterns
Insert here patterns that you want to be searched from your query sequence and their pairwise aligned homologs.

Maximum length of the sequences

The parameter maximum length of the sequence determines the absolute maximum length of all the sequence for needs of visualization. The upper limit has been set to 3000 bp (800 bp for saccharomyces cerevisiae), so you can't determine the sequence to be longer than this. Nevertheless, shorter sequence limits are allowed.

Parameter has a following effect on your query. If your query sequences (and homologous sequences found to correspond your sequence) are longer than the value of the parameter, the sequences will be cut from 5' end. The sequences are expected to be given as 5'->3' form. This is because this program is specially designed for analysis of promoter areas.


Overlapping
Whether overlapping patterns are reported or not, can be selected by chosing the correct radio button.

Organism

Tracker searches information from two separate databases: homology database and sequence database. In this drop down menu you have two possible options per organisms to choose from.

When using this menu you have to make two decisions. First you have to select an organism according to sequences you used as input. Therefore if you have provided sequences that are from mus musculus genome, you have to select one or other of mus musculus options. This way the homologs of your query sequence can be retrieved from the correct database.

The second decision is about which of the two options to use within a certain species. This selection determines from which sequence database the sequences of homolog sequences are being fetcht. The option with 'full' extension contains more sequences but they are not as reliable as the sequences from the database 'clean'


E value threshold

E value parameter has an effect on your analysis only if you have provided the sequence information to our program as fasta formatted sequence data. By using given sequences as an input the program runs a blast run. Only those blast hits which E value is same or lower than the limit are shown to the user.

However, if the amount of valid blast hits exceeds the count of ten, only the 10 first blast hits according to blast's result file are shown to the user.



This tool was developed by Matti Kankainen and Päivi Rosenström, University of Helsinki
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© 2006 University of Helsinki