14 de junio de 2018

updated footprintDB motifs

Hi,
I have just updated the format of footprintDB motifs used in RSAT (www.rsat.eu), which can de downloaded from http://floresta.eead.csic.es/footprintdb/download. This was done to ensure compatibility with compare-matrices in RSAT. Now, motifs look this:

AC  AY750993/VRN1/EEADannot
XX
ID  AY750993:VRN1:EEADannot
XX
NA  AY750993
XX
DE  AY750993
XX
OS  Hordeum vulgare cv Strider
XX
BF  10127;
XX
P0      A      C      G      T
01     19     72      7      2      C
02     10     71      7     12      C
03     57     17     14     12      a
04     56      6     32      6      r
05     94      2      4      0      A
06     84      1      3     12      A
07     79      7      7      7      A
08     57      4      9     30      w
09     24      0     76      0      G
10     15      0     85      0      G
XX
LN  http://floresta.eead.csic.es/footprintdb/index.php?motif=AY750993:VRN1:EEADannot
XX
RN  [1];
RL  Deng W, Casao Mc, Wang P, Sato K, Hayes PM, Jean Finnegan E, Trvaskis B (2015) Direct links between the vernalization response and other key 
traits of cereal crops. Nat Comm 6:5882
RN  [2];
RX  PUBMED: 24234003
RL  Sebastian, A., Contreras-Moreira, B. footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. Bio
informatics 30, 258-65 (2014).
XX

Note that the ID field was added and that a URL pointing to the relevant database entry identified with it is attached. The accession code replaces ':' with '/' to ensure that downstream RSAT analyses can be carried out just fine,
cheers,
Bruno