Guidelines to use Cremofac web-database effectively

Q.1 How do I Search for a particular factor and what are the various query options?

Ans.1 By clicking on the 'Simple Search' option (link under 'Search Database' option), any factor and the organism can be selected. Redundant or non-redundant sequences may be selected as the case may be. To query the database through other forms the 'Advanced Search' option is avaiable (link under 'Search Database' option). This allows for search for factors based on the family that they belong to and the organism that they are found in, as well as for all the ATP dependent or Non-ATP dependent factors found in a given organism. Option to search for factors through protein sequence homology (avaiblable under the advanced search option) is also provided. In this case, the protein sequence may be pasted in the box provided. The result would show all the sequences identically homologous to the entered sequence. The sequence entered is expected to be a subset of atleast one of the protein sequences in the database, i.e. if 'str' represents the sequence entered by the user, and 'SEQ' the one in the database, the program matches the pattern '*str*' against 'STR'.

Various queries which can be fabricated using 'Simple and Advanced Search' options are as below:

    • Queries which can be formed using 'Simple Search' :
      1. Search for 'redundant' sequences belonging to the factor 'abc' found in 'ALL' organisms.
      2. Search for 'non-redundant' sequences belonging to the factor 'abc' found in 'ALL' organisms.
      3. Search for 'non-redundant' sequences belonging to the factor 'abc' found in 'xyz' organism.

    • Queries which can be formed using 'Advanced Search' :
      • Search by family name:
        • Search for 'redundant' remodeling factor sequences belonging to the family 'abc' found in 'ALL' organisms.
        • Search for 'non-redundant' remodeling factor sequences belonging to the family 'abc' found in 'ALL' organisms.
        • Search for 'non-redundant' remodeling factor sequences belonging to the family 'abc' found in 'xyz' organism.
      • Search by organism name:
        • Search for 'non-redundant', 'ATP dependent' remodeling factor sequences found in 'ALL' organisms.
        • Search for 'non-redundant', 'Non-ATP dependent' remodeling factor sequences found in 'ALL' organisms.
        • Search for 'ALL, non-redundant' remodeling factor sequences found in 'ALL' organisms.
        • Search for 'non-redundant', 'ATP dependent' remodeling factor sequences found in 'xyz' organism.
        • Search for 'non-redundant', 'Non-ATP dependent' remodeling factor sequences found in 'xyz' organisms.
        • Search for 'ALL, non-redundant' remodeling factor sequences found in 'xyz' organisms.
        • Search for 'redundant', 'ATP dependent' remodeling factor sequences found in 'ALL' organisms.
        • Search for 'redundant', 'Non-ATP dependent' remodeling factor sequences found in 'ALL' organisms.
        • Search for 'ALL, redundant' remodeling factor sequences found in 'ALL' organisms.
        • Search for redundant', 'ATP dependent' remodeling factor sequences found in 'xyz' organism.
        • Search for 'redundant', 'Non-ATP dependent' remodeling factor sequences found in 'xyz' organisms.
        • Search for 'ALL, redundant' remodeling factor sequences found in 'xyz' organisms.
      • Search for sequences homologous to a sequence entered by the user, for example the sequence 'ALLREVEELKSLMAARDGELEAR' is homologous to the sequence
        gi|9759454| unnamed protein product [Arabidopsis thaliana]
        MLLKFEASSELRLVDPSVSLTVLRKIRLSHLPDMTMTSESSGKKCGEGDGKVAGKSQRKVGLVYDETMCK
        HDTPNGKVDVECPDRIRVIWEKLQLAGVTQRCVVLGGSKAEDKHLKLVHTKKHVNLVKSISTKKKDSRRN
        KIASQLDSIYLNGGSSEAAYLAAGSVVKVAEKVAEGELDCGFAIVRPPGHHAESDEAMGFCLFNNVAVAA
        SFLLNERPDLDVKKILIVDWDIHHGNGTQKMFWKDSRVLIFSVHRHDHGSFYPFGDDGDFNMVGEGPGEG
        FNINVPWEQGGCGDADYLAVWNHILIPVTKEFKPDIILLSAGFDAAIGDPLGGCCVTPYGYSVMLKKLME
        FAHGKIVLALEGGYNLESLGKSSLACVQVLLEDKQIHGSSETYPLESTRRVIQAVRERLCTYWPSLDASM
        ASNENLKNPSAERNSADALLREVEELKSLMAARDGELEARRKELKAKNKELEANEKELEAGLMLIRARED
        VICGLHAKIESLQQERDEAVAKAERIDKELQEDRARSQEFKEDTEFCLSTLRREKELAIMAKNKDLEAKE
        KELEARLMLVHAREDKIHAKIERLQQERDEAVAKAERIDKELQEDRSRSRVGNGSFAFSQEFYEDMDLDE
        LEPLSPEFNEDMDSEELEPFQVIKKNMERSHKKFIKDMECIKFIAIMAMAGESSGKKIGDCDGKVAGNRQ
        RKVGLIYDETMCKHDTPDGEDHPECPDRIRVIWEKLQLAGVSQRCVVLGSSKAEDKHLQLVHTKDHVNLV
        KSISTKQKDYRRNRIASQLNSIYLNGGSSEAAYLAAGSVVKLAEKVAEGELDCGFAIVRPPGHHAEADEA
        MGFCLFNNVAVAASFLLNERPDLGVKKILIVDWDVHHGNGTQKMFWKDPRVLFFSVHRHEYGGFYPAGDD
        GDYNMVGEGPGEGFNINVPWDQGRCGDADYLAAWDHILIPVAREFNPDVIFLSAGFDAAINDPLGGCCVT
        PYGYSVMLKKLMEFAQGKIVLALEGGYNLDSIAKSSLACVQVLLEDKQIQGPPEAYPFESTWRVIQAVWL
        YIILSFNFLISQSETTFHKWAVVLMLLVDQNSSVSCGFRCARGYAHIGLHLQMNYRGS
      • For search by homology, please enter sequence in FASTA format without any definition line.
Q.2 How do I download sequences in Flat File Format ?
Ans.2 The database provides options to download sequences wherever possible. In most cases, this can be achieved by clicking the button in blue background labelled as 'Download sequences in FASTA' or 'Save protein sequence to disk.' These sequences can also be viewed if need be as text files. The snapshot below would further make it clear.
About Chromatin Remodeling Pathways and Acetylation Deacetylation Pathway
The Chromatin Rendeling Pathway is an image showing the signalling,chromatin remodelling assembly and activation of transcription. This image has been taken from the BioCarta Database. All the remodeling factors shown are clickable and hyperlinked to the Korean Unigene Database. The same has also been done for the image showing Acetylation and Deacetylation Pathway.
About Chromatin Remodeling Complexes

All the complexes in the image showing the Remodeling complexes in Human, Drasophila and Yeast are also clickable so as to lead the user to retrieve further information about them from various other web pages.


Note: Here's a list of all the databases that have been referred :
Saccharomyces Genome Database (SGD)- Saccharomyces Genome Database
PIN Database- http://pin.mskcc.org/home.html
OrganelleDB- http://organelledb.lsi.umich.edu/
Flybase - http://flybase.bio.indiana.edu/
HUGO- http://www.gene.ucl.ac.uk/nomenclature/