MAST returns incorrect alignment diagram from DREME

15 views
Skip to first unread message

Esteban Peguero

unread,
Jul 31, 2017, 4:39:45 PM7/31/17
to MEME Suite Q&A
Hello,
I'm trying to scan a set of motifs (discovered using DREME) with MAST, but the alignment diagrams are incorrect in the MAST output:

11_115384558_115384668|Sumo2

  LENGTH = 111  COMBINED P-VALUE = 4.18e-02  E-VALUE =      2.3

  DIAGRAM: 111



5_40005230_40005342|Hs3st1

  LENGTH = 113  COMBINED P-VALUE = 4.26e-02  E-VALUE =      2.3

  DIAGRAM: 113



2_91460599_91460720|Ckap5

  LENGTH = 122  COMBINED P-VALUE = 4.61e-02  E-VALUE =      2.5

  DIAGRAM: 122




Example DREME:



# DREME 4.11.3

#     command: dreme -dna -p neurite.fasta -n soma.fasta -oc ./DREME_neurite -e 1 -mink 3 -maxk 10 -norc

#   positives: 54 from neurite.fasta (Fri Jul 28 11:16:55 CEST 2017)

#   negatives: 76 from soma.fasta (Fri Jul 28 11:16:55 CEST 2017)

#        host: sl-cheku-p-cs1

#        when: Mon Jul 31 21:17:40 CEST 2017


MEME version 4.11.3


ALPHABET "DNA" DNA-LIKE

A "Adenine" CC0000 ~ T "Thymine" 008000

C "Cytosine" 0000CC ~ G "Guanine" FFB300

N "Any base" = ACGT

X = ACGT

. = ACGT

V "Not T" = ACG

H "Not G" = ACT

D "Not C" = AGT

B "Not A" = CGT

M "Amino" = AC

R "Purine" = AG

W "Weak" = AT

S "Strong" = CG

Y "Pyrimidine" = CT

K "Keto" = GT

U = T

END ALPHABET


strands: +


Background letter frequencies (from dataset):

A 0.227 C 0.273 G 0.259 T 0.242



MOTIF TTTTRD DREME


#             Word    RC Word        Pos        Neg    P-value    E-value

# BEST      TTTTRD     HYAAAA         45          2   2.4e-023   1.5e-018

#           TTTTGA     TCAAAA         17          0   5.8e-008   3.6e-003

#           TTTTGT     ACAAAA         17          0   5.8e-008   3.6e-003

#           TTTTAA     TTAAAA         19          1   8.5e-008   5.3e-003

#           TTTTAT     ATAAAA         16          0   1.7e-007   1.1e-002

#           TTTTAG     CTAAAA          9          0   2.4e-004   1.5e+001

#           TTTTGG     CCAAAA          7          1   8.9e-003   5.6e+002


letter-probability matrix: alength= 4 w= 6 nsites= 130 E= 1.5e-018

0.000000 0.000000 0.000000 1.000000

0.000000 0.000000 0.000000 1.000000

0.000000 0.000000 0.000000 1.000000

0.000000 0.000000 0.000000 1.000000

0.584615 0.000000 0.415385 0.000000

0.446154 0.000000 0.146154 0.407692


I also used the web version of MAST, but again the alignments in the HTML file are not shown.


http://meme-suite.org/info/status?service=MAST&id=appMAST_4.12.01501533185562-749754134


Thank you.

CharlesEGrant

unread,
Aug 7, 2017, 2:12:33 PM8/7/17
to MEME Suite Q&A
I'm afraid I don't understand your question. You may be mis-understanding the function of MAST. MAST is not producing alignment diagrams for the motifs, rather it is identifying the sequences that have the best overall match to the collection of motifs you've provided. The block diagram generated by MAST show only the motif matches with a p-value < 0.0001, and only for the highest scoring sequences.

This post on the differences between MAST and FIMO may be helpful:


Reply all
Reply to author
Forward
0 new messages