these changes are in response to the rapidly increasing number of available ribosomal rna gene sequences ( rrna sequences ) and the trend toward high - throughput rrna sequencing with the concomitant need for high volume rrna analysis tools . details about the data and analysis services can be found at the rdp - ii website ( http://rdp.cme.msu.edu/ ) . the rdp obtains bacterial rrna sequences from the international nucleotide sequence databases ( insd : genbank / embl / ddbj ) on a monthly basis . these sequences are aligned against a general bacterial rrna model using a modified version of rnacad ( 2 ) , a stochastic context free grammar ( scfg)-based rrna aligner that directly incorporates rrna secondary structure information into its internal model . this aligner is trained on a set of high - quality hand - aligned sequences and incorporates the conserved bacterial secondary structure model of gutell and co - workers ( 3 ) . as of release 9.21 ( august 2004 ) , the database contained 101  632 total small subunit bacterial rrna sequences . of these , 39  772 were near full - length ( 1200 bases ) , 54  316 came from uncultured organisms and 4431 were from type strains of validly named bacterial species . all release 9 tools use a new hierarchical framework ( rdp hierarchy ) differing significantly from the hierarchy provided with previous rdp releases . the rdp hierarchy is based on the new phylogenetically consistent higher - order bacterial taxonomy proposed by garrity et al . it provides a phylogenetic framework into which to place results of the rdp analysis functions , and it provides an entry point for users looking for sequences from specific groups of organisms . new sequences are placed into the rdp hierarchy using the rdp classifier ( see below ) . the rdp analysis services have been completely revised to support the emerging trend toward high - throughput rrna sequence analysis in microbial ecology and related disciplines . the user can choose to apply up to three data filters on the view or analysis . by applying the three filters , the user can ( i ) include only environmental clone or only isolate sequences ; ( ii ) include only sequences 1200 bases in length ( near full - length ) or only shorter sequences ; and ( iii ) include only sequences from type strains or only non - type strain sequences . the latter filter is of special importance since type strains act as a link between rrna - based phylogeny and taxonomy . a more detailed description of each analysis service can be found at the rdp website . the browser presents views of the rdp sequences placed either in the rdp hierarchy , or optionally in the ncbi taxonomy hierarchy ( 5 ) . while navigating , the browser automatically expands an appropriate number of hierarchical levels to fit the display . at any time , the user can select for later download of both individual sequences and those of entire taxa . data filters can be applied at any time to limit the display to specific data subsets . in addition , the user can quickly search for words or phrases in the sequence definition line . this includes the organism name and strain designation ( if available ) , culture collection identifiers and insd nucleic acid accession identifiers . optimized for large query sets , it can be used to give an initial taxonomic placement for a single sequence or hundreds of sequences . the first result page summarizes the assignments on an interactive display similar to that of the hierarchy browser . each node in the hierarchy lists the number of user queries assigned to that taxonomic rank . a confidence estimate is generated for each assignment , and the assignments are displayed only when the estimate is above a user - specified confidence threshold . at any time , the user can switch to a detail view showing the detailed taxonomic assignments and confidence scores for any subset of query sequences . these assignment details can also be downloaded in a file suitable for import into popular spreadsheet programs . sequence match is a complete re - implementation of the original sequence match method ( 1 ) . sequence match finds sequences similar to a user 's query sequences using a word matching strategy not requiring prior alignment . sequence match is more accurate than blast ( 6 ) at finding closely related rrna sequences ( table 1 ) . the related sequences returned by sequence match serve as a good starting point for more detailed examination of relatedness by classical phylogenetic or other methods . the initial result page presents a k - nearest neighbor ( k - nn ) classifier assignment of the query sequences . a query is assigned to the lowest taxonomic rank that includes the k highest scoring database sequences . the value of k , as well as the three data filters can be changed at will in this view . the user can switch from the summary k - nn view to a detailed results view for any query sequence . in this view , the top k database matches to the query are displayed in the rdp hierarchy . in this mode , any subset of the matches can be selected for transfer to the hierarchy browser and later download . probe match is a complete re - implementation of our previous probe match program ( 1 ) . it uses a more efficient algorithm that is better suited to the amount of rrna data available today and in the foreseeable future . the new probe match accepts a candidate primer / probe , optionally with ambiguity codons , of up to 64 bases in length . while our previous version searched for hits within a specified number of mismatches ( hamming distance ) , the new version finds hits with a combination of mismatches and insertion / deletions ( edit distance ) . since some single insertion / deletion may be no more deleterious than a single mismatch , this new capability offers a significant improvement in the detection of potential cross - hybridization . in our previous implementation , the high percentage of partial sequences in the database limited the program 's utility ; it was difficult to determine if database entries failed to match simply because the sequence was incomplete in the target region . in this new version , the users can restrict analysis to database entries containing sequence data for the candidate probe target region of the rrna molecule . ( however , the search is not limited to this region of the molecule . ) similar to the other new programs , the results are displayed in an interactive version of the rdp hierarchy . each taxonomic rank lists the total number of sequences searched and the number matching within a user - specified edit distance . the rdp analysis services have been completely revised to support the emerging trend toward high - throughput rrna sequence analysis in microbial ecology and related disciplines . the user can choose to apply up to three data filters on the view or analysis . by applying the three filters , the user can ( i ) include only environmental clone or only isolate sequences ; ( ii ) include only sequences 1200 bases in length ( near full - length ) or only shorter sequences ; and ( iii ) include only sequences from type strains or only non - type strain sequences . the latter filter is of special importance since type strains act as a link between rrna - based phylogeny and taxonomy . a more detailed description of each analysis service can be found at the rdp website . the browser presents views of the rdp sequences placed either in the rdp hierarchy , or optionally in the ncbi taxonomy hierarchy ( 5 ) . while navigating , the browser automatically expands an appropriate number of hierarchical levels to fit the display . at any time , the user can select for later download of both individual sequences and those of entire taxa . data filters can be applied at any time to limit the display to specific data subsets . in addition , the user can quickly search for words or phrases in the sequence definition line . this includes the organism name and strain designation ( if available ) , culture collection identifiers and insd nucleic acid accession identifiers . optimized for large query sets , it can be used to give an initial taxonomic placement for a single sequence or hundreds of sequences . the first result page summarizes the assignments on an interactive display similar to that of the hierarchy browser . each node in the hierarchy lists the number of user queries assigned to that taxonomic rank . a confidence estimate is generated for each assignment , and the assignments are displayed only when the estimate is above a user - specified confidence threshold . at any time , the user can switch to a detail view showing the detailed taxonomic assignments and confidence scores for any subset of query sequences . these assignment details can also be downloaded in a file suitable for import into popular spreadsheet programs . sequence match is a complete re - implementation of the original sequence match method ( 1 ) . sequence match finds sequences similar to a user 's query sequences using a word matching strategy not requiring prior alignment . sequence match is more accurate than blast ( 6 ) at finding closely related rrna sequences ( table 1 ) . the related sequences returned by sequence match serve as a good starting point for more detailed examination of relatedness by classical phylogenetic or other methods . the initial result page presents a k - nearest neighbor ( k - nn ) classifier assignment of the query sequences . a query is assigned to the lowest taxonomic rank that includes the k highest scoring database sequences . the value of k , as well as the three data filters can be changed at will in this view . the user can switch from the summary k - nn view to a detailed results view for any query sequence . in this view , the top k database matches to the query are displayed in the rdp hierarchy . in this mode , any subset of the matches can be selected for transfer to the hierarchy browser and later download . probe match is a complete re - implementation of our previous probe match program ( 1 ) . it uses a more efficient algorithm that is better suited to the amount of rrna data available today and in the foreseeable future . the new probe match accepts a candidate primer / probe , optionally with ambiguity codons , of up to 64 bases in length . while our previous version searched for hits within a specified number of mismatches ( hamming distance ) , the new version finds hits with a combination of mismatches and insertion / deletions ( edit distance ) . since some single insertion / deletion may be no more deleterious than a single mismatch , this new capability offers a significant improvement in the detection of potential cross - hybridization . in our previous implementation , the high percentage of partial sequences in the database limited the program 's utility ; it was difficult to determine if database entries failed to match simply because the sequence was incomplete in the target region . in this new version , the users can restrict analysis to database entries containing sequence data for the candidate probe target region of the rrna molecule . ( however , the search is not limited to this region of the molecule . ) similar to the other new programs , the results are displayed in an interactive version of the rdp hierarchy . each taxonomic rank lists the total number of sequences searched and the number matching within a user - specified edit distance . the rdp - ii data and analysis services can be found at http://rdp.cme.msu.edu/. the rdp 's mission includes user support . the rdp - ii staff may also be contacted via fax ( + 1  517  353  8957 attn : rdp ) or regular mail . we thank several individuals for their past contributions : robin gutell ( and his colleagues ) , chuck parker , paul saxman , bonnie maidak , tim lilburn , niels larsen , tom macke , michael j. mccaughey , ross overbeek , sakti pramanik , scott dawson , mitch l. sogin , gary olsen and carl woese . the rdp is supported through us doe ober / nih grant de - fg02 - 99er62848 and nsf grant dbi-0328255 .