MAST -- Motif Alignment and Search Tool

Motif search tool

The input to MAST contains the following fields.

  • motifs
    This is the name of a file on your computer that contains one or more of motifs that characterize a group of related sequences. This will normally be the name of a file that contains the results of a MEME analysis. If you wish to use motifs from another source it must be first converted to a compatble format. A "browse" button is provided by MAST to help you locate the motif file you wish to use.
  • treatment of reverse complement strands
    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.):
    1. 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.)
    2. 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.
    3. 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.
  • use individual sequence composition in E-and p-value calculation
    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.
  • ignore motifs with high E-values
    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. The default threshold will cause MAST to use all motifs in the query, regardless of their E-values.
    Note: This option is only available for motifs generated by MEME 3.0 and above.
  • search nucleotide database with protein motifs
    Choosing this option will cause MAST to search the nucleotide version of the selected sequence database, converting the nucleotide sequences to protein sequences in all six reading frames. By default, MAST searches the protein version of the selected database when you give it a file of protein motifs.
  • scale motif display threshold by sequence length
    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.
  • E-value display threshold
    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.
Search using MAST
MAST introduction
MEME SUITE introduction