a constant flood of new genomic information has brought a new age of discovery to biology .
unfortunately , this deluge of new data is rarely fully utilized , in part because bench scientists find it increasingly challenging to maintain a current , integrated picture of the latest data .
this problem is particularly pronounced for scientists who study large numbers of potentially interesting molecules , a common result of microarray - based or proteome - based experiments .
regularly updating such data by hand can be extremely burdensome and is rarely done . as a result , many scientists work unaware of newly discovered annotation , homologs , clones or protein domains that could further their research .
current comparative table , or cct , is a web - based application designed to solve this problem by displaying the most up - to - date results of customized genomic searches in a convenient table .
it can be easily configured to automatically download new versions of databases and to run any number of bioinformatics searches on the new data .
cct then organizes the results in a table containing hyperlinks color - coded by result age , making it simple to pick out recently changed results .
this allows scientists to continuously harvest potentially useful data about any set of sequences of importance to their research .
cct joins a number of other excellent servers whose aim is to manage data overload ( 1,2 ) , but cct has unique strengths .
the most widely used of these other services , pubcrawler , searches for text and literature matches in pubmed , genbank or both but does not perform actual sequence searching ( 3 ) .
servers that do allow sequence searches ( e.g.   and ) allow the searching of prescribed subsets of public databases and/or a single private database of each data type that is uploaded manually ( 2 ) .
like myhits and swiss - shop , cct performs sequence - based searches , but it uniquely offers a local installation , allowing independence from remote servers .
other novel features of cct include automated highlighting of even small changes in data files , a simple interface for scientists interested in multiple sequences and the ability to monitor any number of databases to which the user has access .
the computer has a 3 ghz processor , 200 gb of hard drive space and 2 gb of ram .
mac os x compatibility was tested on a dual 2 ghz g5 tower with 1.5 gb of ram , a 160 gb hard drive and mac os x 10.3.4 .
cct is implemented in perl and makes heavy use of the bioperl toolkit ( 4 ) .
a demonstration of cct and an installation guide are available at , and the software is freely available from .
a scientist typically begins using cct by adding three types of data through a web interface : ( i ) a file containing sequences of interest , ( ii ) database location(s ) to monitor for updates and ( iii ) searches to perform .
although cct can be run at will , it is typically run automatically . in this mode ,
cct periodically ( e.g. once per day , such as at 1 a.m. ) checks user - selected databases and downloads updated versions as they become available .
cct then runs user - selected searches on these data and builds a table with one row for each sequence and one column for each database searched ( figure 1 ) .
each cell contains links to the results of each search , color - coded by the length of time since a change in data has affected the search results .
in addition , when a result is updated , the new result is compared with the previous one , and differences are highlighted in the new data file ( figure 2 ) . taken together , link coloring and difference highlighting allow numerous search results to be quickly scanned and evaluated for novelty ( or for stability over time ) .
this feature is valuable for scientists engaged in ongoing projects as well as those deciding when to commit limited laboratory resources to the characterization of a set of interesting but preliminary sequences .
cct can be run locally or remotely via the internet and comes bundled with wrappers for six different bioinformatics search programs .
hmmpfam is a wrapper for the hmmpfam tool and is useful for automating searches of sequences against ever changing protein domain databases such as pfam ( 5 ) .
tblastn and blastp are the software 's wrappers for ncbi 's blast searches ( 6 ) .
the seq program is specific to cct and is useful for isolating regions of the genome , e.g. for finding genes and open reading frames .
seq takes tblastn or blastp output , captures the sequences for the target blast high - scoring pairs and extends them out to a user - specified delimiter .
for example , if a stop codon were selected , seq would capture the sequence of the flanking open reading frame .
revblast uses seq output as a query to blast search another database , permitting reciprocal blasting , a common method for finding ortholog pairs ( 7 ) .
finally , the homolog program takes revblast output and uses clustal - w ( 8) to generate a pairwise alignment if sequence pairs meet user - specified parameters .
when used together , these programs are an effective tool for finding orthologs and can be customized in a way that sets cct apart from other comparative genomics tools ( 9 ) .
the mac os x version of cct can be installed in 60 s in a few simple steps from a double clickable install package .
it is fully self - contained and includes code for bioperl , clustal - w , blastall and hmmpfam .
the linux version does not include this code in the expectation that linux users may want to integrate cct into existing bioinformatics resources on their servers .
cct 's user manual is part of every installation and can also be found at the software 's demo site .
the user manual contains an installation guide , a beginner 's guide , the addresses of sample databases , screenshots and other useful information .
in addition , cct is installed with a link to extensive code documentation to make its customization as easy as possible for users with any level of programming experience .
programmers can construct new program modules to interact seamlessly with cct using an included template file .
the design of cct falls into two main parts : the web interface and the script runcct.pl .
users can add and delete tables , searches and databases , and can view their data by browsing a cct web page .
runcct.pl controls most of cct 's daily work , such as downloading databases , running searches and updating tables .
this script can also be called manually from the command line and can be manipulated to perform only certain steps of its process or run only specified searches .
cct is freely available to all and it will continue to be developed ( ) .
cct can be a very useful tool for scientists who study large sets of genes in today 's evolving genomic landscape . by empowering non - bioinformaticians to automate custom searches and examine current results at a glance
, cct allows a remote database submission in the evening to influence the next morning 's bench experiment .
the molecule and description columns contain information supplied by the user ; the other columns contain data generated by automated searches against user - specified databases . in these database columns ,
links are color - coded to reflect the length of time since the search result last changed . to generate the table shown ,
cct was given a set of 48 genes in the mycobacterium tuberculosis ( mtb ) dormancy regulon ( 10 ) and directed to monitor four remote databases ( pfam , the mtb proteome and two incomplete genomes , m.smegmatis and m.marinum ) .
the pattern of red indicates that a new release of the m.marinum genome was downloaded in the past 24 h ( generating many new red tblastn links ) , and that a new sequence ( seq program ) of an ortholog ( homolog program ) was found for the tb protein rv1812c .
the predicted ortholog for rv0079 , in contrast , did not change as a result of the update and the corresponding links remain blue .
more detail concerning any result can be viewed by clicking on the corresponding link(s ) .
example of a result file revised to reflect a new release of the pfam database .
the regions above and below the horizontal line show different parts of the same result file .
this hmmpfam search result shows that the  conserved hypothetical protein rv2030c matches a new domain in pfam , specifically the 
phosphoribosyl domain has been changed subtly ( note the changed amino acids in the subject line ) . taken together with the change in database size for the new release ,
the e - value for this search has changed somewhat . to view the newest results only ( without highlighting to show changes )
 the current comparative table ( cct ) software program enables working biologists to automate customized bioinformatics searches , typically of remote sequence or hmm ( hidden markov model ) databases . 
 cct currently supports blast , hmmpfam and other programs useful for gene and ortholog identification . 
 the software is web based , has a bioperl core and can be used remotely via a browser or locally on mac os x or linux machines . 
 cct is particularly useful to scientists who study large sets of molecules in today 's evolving information landscape because it color - codes all result files by age and highlights even tiny changes in sequence or annotation . by empowering non - bioinformaticians to automate custom searches and examine current results in context at a glance 
 , cct allows a remote database submission in the evening to influence the next morning 's bench experiment . 
 a demonstration of cct is available at   and the open source software is freely available from . 
INTRODUCTION
MATERIALS AND METHODS
USAGE
Figures and Tables