MAST - Submission form

Select this option if you have protein motifs but DNA sequences. The DNA sequences will be translated on the fly to protein at each frame for comparison with the motifs.

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Select this option if you want MAST to remove any motifs that are too similar to other motifs in your query. Having pairs of motifs that are too similar will cause the E-values computed by MAST to be inaccurate. If you don't select this option, problematic motifs will be highlighted in your MAST output.

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MAST only displays sequences matching your query with E-values below the given threshold you specify here. By default, sequences in the database with matches with E-values less than 10 are displayed. If your motifs are very short or have low information content (are not very specific), it may be impossible for any sequence to achieve a low E-value. If your MAST search returns no hits, you may wish to increase the E-value display threshold and repeat the search.

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MAST can ignore motifs in the query with E-values above a threshold you select. This is desirable because motifs with high E-values are unlikely to be biologically significant. If this option is disabled then MAST will use all the motifs in the query, regardless of their E-values.

This option only works for motifs where the E-value is included in the motif file. MAST does not have any capability for re-assessing the signficance of a motif.

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This option can improve search selectivity when erroneous matches are due to biased sequence composition.

MAST normally computes E-values and p-values using a random sequence model based on the overall letter composition of the database being searched. Selecting this option will cause MAST to use a different random model for each target sequence. The random model for each target sequence will be based on its letter composition, not that of the entire database.

Using this option will tend to give more accurate E-values and increase the E-values of compositionally biased sequences. This option may increase search times substantially if used in conjunction with E-value display thresholds over 10, since MAST must compute a new set of motif score distributions for each high-scoring sequence.

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MAST displays motifs that score above a threshold for all high-scoring sequences. By default, this threshold is based on the probability of the motifs without regard to the length of the sequence. The threshold was chosen with protein sequences of average length in mind. Consequently, many positions in very long sequences may match motifs with scores above this threshold by chance, making the results difficult to interpret.

Selecting this option causes the motif display threshold to take sequence length into account. This will reduce the number of weak motifs displayed in long sequences and minimize the size of the output file.

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MAST can automatically generate the reverse complement strand for each nucleotide sequence in the database and treat it in three different ways. ("Given strand" refers to the sequence as it appears in the database MAST is searching.):

combine with given strand
  MAST searches for motif occurrences on either the given strand or its reverse complement together, not allowing occurrences on the two strands to overlap each other, and displays them together as a single sequence. This allows motifs to occur on either strand and still count toward the overall E-value of the match. (The given strand is the sequence as it appears in the database MAST is searching.)
treat as separate sequence
  MAST to search for motifs in both the given strand and its reverse complement, treating them as two, independent sequences. As of version 4.3.2 the results are displayed together in the html though in previous versions the results were displayed separately for the two strands, as though both had occurred in the database.
none
  MAST searches only the given strand of each sequence in the database.

Note: this field has no effect when the database contains protein sequences.

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MAST - Motif Alignment & Search Tool
../doc/images/mast_icon.png: MAST Logo

Data Submission Form

Find sequences that match a set of motifs.

motifs
Input the motifs
FILE register_component

sequences
Input the sequences
DATABASE
register_component

### Reverse-complement strand handling

RC strand handing:

### Translate DNA sequences to protein?

Search DNA sequences with protein motifs?

### Set a sequence display threshold

Sequence E-value ≤

### Use individual sequence composition?

Use per sequence composition in significance calculation?

### Scale the motif display threshold?

Scale motif display threshold by sequence length?

### Filter motifs by E-value threshold?

Motif E-value ≤

### Remove redundant motifs from query?

Should MAST remove any motifs that are too similar to others?