MAST Introduction

The MEME Suite is a service required for searching and describing motifs in DNA or RNA sequences. This service is very convenient because, firstly, it works stably and also contains many tools for data analysis. A list of these tools is presented below:

1. MEME (Multiple EM for motif elicitation) is a tool for searching de novo motives. It accepts a file in fast format as input, searches for motifs from 6 to 50 nucleotides in length (the length is specified by the user). The disadvantage is that you cannot enter a ready-made motive and ask to find it in the sequences. Positive features: the ability to set a “negative” search – that is, to exclude a certain motive from the search. You can also set the option to search for palindromes only or search only on one of the nets (forward or backward).
2. MAST (Motif alignment and search tool) – a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs.
3. TOMTOM (Motif comparison tool) – compares one or more motifs against a database of known motifs.
4. GOMO (Gene ontology for motifs) is a service that can find the input motif in the format of a matrix of weights in organisms whose genomes are well annotated (at the moment these are the genomes of 5 eukaryotes, among which there are Homo sapiens) and issue a GO gene identifier in which this motive was found.
5. GLAM2 (Gapped local alignment for motifs) – sequences are sent to the input and motives are looked for in them, but the restriction on the absence of gaps in motives is removed.
6. GLAM2SCAN (Scanning with gapped motifs) – a motif with gapped motifs in the format of a matrix of weights is sent to the input, but the search is carried out in a database. The service can work with the NCBI ftp server, taking data directly from there.
7. FIMO (find individual motif occurence) – finds motives for individual genes (the output is MEME – a matrix of weights), it works rather poorly. It produces a table of found motives for individual genes, but there are a lot of obviously false results in this table.
8. MCAST (Motif cluster alignment search tool) – searches sequences for clusters of matches to one or more nucleotide motifs (sample output for motifs and sequences).
9. MEME-ChIP (Motifs analysis for large DNA database) – a version of MEME, made specifically for the search for motifs in the data obtained from ChIP-seq during sequencing. Quite large files can be submitted to the input, which a regular MEME would not be able to handle. The next 3 services also work with ChIP-Seq data.
10. SPAMO (Spaced motif analysis tool) – analyzes the enrichment of motif spacings instead of occurrences.
11. DREME (Discriminative DNA motif discovery) – discovers short, ungapped motifs that are relatively enriched in your sequences compared with shuffled sequences or your control sequences.
12. CentriMo (Central motif enrichment analysis) – can perform either central or local motif enrichment analysis.