the aim of designing biras is to make full use of the retrieval function of entrez and timely retrieve the latest information of literatures and gene sequences .
usually , when we retrieve a keyword or term by entrez web server in ncbi , we will first get a summary list of literatures and gene sequences .
if we find the necessary literatures and sequences , we will click their links and read the detailed information .
the first step is to send the keyword or term to the entrez web server and gets the identify ( i d ) list of the newly increased literatures and sequences .
secondly , it retrieves each i d and saves the retrieval information to local disk .
thus , biras effectively retrieved user - defined updating information of the literatures and gene sequences .
the medline literatures , nucleotide sequences and protein sequences retrieval section of biras provides the complex term retrieval function of entrez ( http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html ) .
researchers can retrieve not only the simple single term but also the logical field composed of several terms with boolean operators  and , or , not  .
furthermore , biras also provides some common download styles ( literatures : abstract , asn.1 , citation , medline , summary ; nucleotide sequences : asn.1 , fasta , genbank , report , summary ; protein sequences : asn.1 , fasta , genpept , report , summary ) .
thereby , biras provides a quite convenient retrieval mode for the researchers who concern with the special literatures and sequences . besides , biras provides the simple way for browsing the updating literatures and sequences , and shows impact factor of each journal as an especial item to make provide various kinds of information for the user ( fig .
to the researchers who are studying structure and function of novel genes , it is very important for them to know whether there is any new sequences with high homology to their - concerned genes in the public genbank database .
such sequences often come from homology genes of different species or alternative splicing forms of the same gene .
therefore , biras provides an information retrieval mode based on the user - defined sequence . in other words ,
biras automatically uses blast program from the web server at ncbi to find out related gene sequences or protein sequences that are homologous to the sequence in genbank .
it is quite convenient for users to retrieve timely based on the homology of sequences .
as far as the process of analysis , biras adopts the qblast s api to access the ncbi qblast system ( http://www.ncbi.nlm.nih.gov/blast/doc/urlapi.html ) , and uses the corresponding blast program of the ncbi qblast system for analysis .
when the ncbi qblast process is finished , biras will automatically save the result to local disk .
after then , biras does some necessary treatments with the analysis result and inform users of the latest increased homolog sequences in the genbank database . to automatically analyze sequence homology
biras allows users to set four common analysis parameters : database , expect , descriptions , and alignments 4 .
, 5 .. researchers can set these parameters according to their demands in order to get the valid analysis result .
according to the above requirements , our designed biras has the following interface ( fig .
users can adjust the parameters of update conditions in the menu  set / update set 
, specify the server for sending e - mail in the menu  set / mail set  , and define the same or different e - mail addresses for any retrieval item in the menu  set / mail address  . thus ,
when the certain item retrieval finds out the updated information , biras can send update information as attachments in html format to the user - defined e - mail addresses , in order to make users receive the latest information as early as possible .
the outstanding characteristic of biras program is that it can provide users with required information timely and dynamically according to defined requirements .
users can get the valid information easily enough , but need not download the whole medline database or the whole nucleotide sequences and protein sequences database .
consequently , it obviously conduces to promoting the efficiency of their studies . at present , biras merely concerns with the following contents : 1 ) medline literatures retrieval .
namely , biras timely informs users of the latest related literatures according to the user - defined terms , and shows the impact factor of each journal .
2 ) nucleotide sequences and protein sequences retrieval , which means biras timely retrieves the concerned nucleotide sequences and protein sequences according to the user - defined terms .
if it finds out the new sequences , it will inform users of the information immediately .
3 ) function analysis of special sequences . for this purpose , biras will use the latest database to do some analysis such as homology analysis , structure and function analysis with user - defined sequence .
the analysis result was also sent to users by biras timely . to a certain extent
if user does not initiatively retrieve the entrez web server at ncbi , the latest information will not be known by the users in time .
therefore , our reported biras here is a quite important dynamic information retrieval and analysis system . in other words ,
biras seems to be a worker who works quietly and always transfers user - concerned latest information timely .
therefore , biras could provide users with the maximum information retrieval services in the future .
compared with other similar systems , the real - time feature of literatures and sequences retrieval ability of biras is quite outstanding .
the medline workbench ( http://www.medbench.org/ ; medbench updates ver.3.1 ) allows users to order the information retrieval free service with the user - defined terms .
however , in the practical test that respectively retrieves term  apoptosis  with biras and medline workbench in the same time , biras could find out 20 daily updated literatures in july 10 , 2002 . from then on biras has begun continuously retrieving the updating literatures every day .
however , the medline workbench only sent a confirm e - mail to us within the first 24 hours , and did not contain any updating information .
according to our experiences , in the daily using , the medline workbench merely sent about 1/4 number of literatures information at intervals .
in fact , biras directly connects to the entrez web server of ncbi , and automatically retrieves updating information .
therefore , its performance is superior to those of some existing literature retrieval systems . for the real - time literature retrieval ,
however , the mailing list service has no definite keywords filtering feature . in other words
, the mailing list service of these magazines could only provide users the summary of the latest publications , but can not filter the information automatically according to user - defined terms .
when the user reads the whole content of the journals , it will take a lot of time to judge what they really need or not .
compared with this kind of time wasting , biras can completely retrieve and effectively gather the users concerned information from the databases of the ncbi according to the user - defined term .
obviously , biras has the more practicability . in terms of new sequences and their functions retrieval based on the sequence homology analysis ,
for instance , the swiss shop server ( http://www.expasy.ch/swiss-shop/ ) allows user to specify the protein sequence and do homology analysis , and then returns the analysis result to user by e - mail .
the embl database has ever provided the similar service , and then it stopped the service for some reasons . compared with these resources ,
our sequence homology analysis function of biras includes both the nucleotide sequences homology analysis and protein sequences homology analysis .
furthermore , it can carry out analysis using all databases in ncbi including sequences databases derived from the patent division of genbank , database of expressed sequence tags ( est ) , and databases of high throughput genomic sequences ( htgs ) and so on .
users can freely use these databases by setting different parameters . for realizing the characteristic of running in various operating systems ( windows/ linux / macintosh etc .
) , the core code of biras is written in standard c language , and then joins the corresponding management software based on the individual characteristic of the various operating systems . at present ,
of course , the computers installed with biras should have connected with the internet directly . in conclusion , through many strict tests
, biras can retrieve the information of user - concerned literatures and sequences timely and effectively from the entrez server at ncbi .
in fact , if you can retrieve and gain the information by using the entrez , biras can automatically retrieve them and inform users in time .
thereby , it is believed that biras would be used to retrieve specific information from large amount of biological data in now days .
 the aim of this study is to design a biological information retrieval and analysis system ( biras ) based on the internet . 
 using the specific network protocol , biras system could send and receive information from the entrez search and retrieval system maintained by national center for biotechnology information ( ncbi ) in usa . 
 the literatures , nucleotide sequence , protein sequences , and other resources according to the user - defined term could then be retrieved and sent to the user by pop up message or by e - mail informing automatically using biras system . 
 all the information retrieving and analyzing processes are done in real - time . as a robust system for intelligently and dynamically retrieving and analyzing on the user - defined information 
 , it is believed that biras would be extensively used to retrieve specific information from large amount of biological databases in now days . 
 the program is available on request from the corresponding author . 
The Scheme of Literatures, and Nucleotide Sequences and Protein Sequences Retrieval Based on Entrez
Scheme of Sequence Analysis Based on Blast
Program Design of BIRAS and the Interface
Discussion