| | 52 | [http://meme-suite.org/doc/meme-format.html/ MEME Suite] For protein binding motifs |
| | 53 | * Build a PWM from a series of aligned sequences using the "meme" command |
| | 54 | {{{ |
| | 55 | meme aligned_sequences.txt -protein -nmotifs 1 -w [width of motif] -o location_for_output_matrix |
| | 56 | }}} |
| | 57 | |
| | 58 | Program options: |
| | 59 | -protein: specifies your input sequences are amino acids.\\ |
| | 60 | -nmotifs: indicates the number of motifs to look for in your sequences\\ |
| | 61 | -w: defines a width of a motif to find [optional].// |
| | 62 | |
| | 63 | Using the MAST program within the MEME-suite, with the PWM output by the above command you can search a list of protein sequences, in FASTA format, for your motif. |
| | 64 | {{{ |
| | 65 | mast -minseqs 100 -m 1 -comp -ev 10 -o output_directory |
| | 66 | }}} |
| | 67 | |
| | 68 | Program options: |
| | 69 | -minseqs: Specifies the number of sequences to analyze.\\ |
| | 70 | -m: Specifies the number of motifs within your matrix file.\\ |
| | 71 | -comp: This option can improve search selectivity when erroneous matches are due to biased sequence composition.\\ |
| | 72 | -ev: 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.\\ |
| | 73 | |
| | 74 | |
