basic local alignment search tool ( blast ) is a sequence similarity search program that can be used via a web interface or as a stand - alone tool to compare a user 's query to a database of sequences ( 1,2 ) . several variants of blast compare all combinations of nucleotide or protein queries with nucleotide or protein databases . blast is a heuristic that finds short matches between two sequences and attempts to start alignments from these  hot spots. in addition to performing alignments , blast provides statistical information about an alignment ; this is the  expect value , or false - positive rate . the national center for biotechnology information ( ncbi ) maintains a blast server with a homepage at . on the homepage the different blast searches are listed by type : nucleotide , protein , translated and genomes . the  program selection guide ( ) provides an introduction to the various programs and database options ( 3 ) . when a query is submitted to the ncbi server , either as a sequence in fasta format or as a sequence identifier , e.g. genbank accession number , the search is sent to the blast server and a  request identifier ( rid ) is returned . the query and results are stored in a structured format for up to 24 h after an rid is issued . the rid identifies the search and allows the results to be viewed in several formats , which include the familiar blast report , a simplified  hit table , xml and asn.1 [ ( 4 ) and ] . the number of outstanding jobs from one ip address is taken into account when queuing requests , as described at , so that one user does not monopolize the entire service . searches sent to the server are handled by a sophisticated queuing system that may spread the search over 10 to 20 machines , making the search much faster than if it were run on one machine . more details are available at   we report here on new display features that we have implemented . these include highlighting mismatches between similar sequences , showing where the query was masked for low - complexity sequence and integrating information from the ncbi entrez system ( 5 ) into the blast display . additionally the new report generator has been optimized for databases with large sequences . during the past five years many genomes have become searchable and the sequences in those databases are typically long contigs or chromosomes . additionally many long nucleotide sequences have been added to the blast databases as a result of high - throughput genomic projects . traditionally sequences in the blast database have been associated with only one descriptive phrase that is normally the same as the  definition in the genbank flat file . this means that only very generic information is provided for matches to long database sequences , even though such a sequence might have annotations for many genes , coding regions ( cds ) and other features . the top line of figure 1 shows a database sequence definition and merely states that the sequence is part of human chromosome 6 and is about 48 million bases long . this reveals little about the region of the database sequence containing the match . to address this issue , we now provide feature information for blast alignments involving long database sequences ( currently defined as larger than 200 kb ) . two types of sequence features ( cds and rrna ) are currently supported but this could be expanded to other features . an example is shown in figure 1 where a custom definition line is displayed for each of the two alignments . according to the custom definition lines the query matches a region inside the human major histocompatability complex ( mhc ) a gene , as well as a region that is about 54 kb upstream of the mhc a gene and about 58 kb downstream of the mhc g gene , allowing one to quickly draw the conclusion that the query sequence is highly related to the human mhc . frequently alignments are between very similar sequences and it 's difficult to identify a few mismatches in the pairwise alignment . to address this issue we recently introduced a new format called  pairwise with identities , shown in figure 2 on an alignment with 98% identity between the query and database sequence . a dot indicates identity between the database sequence and query at that position ; mismatches are shown as the database sequence letter in place of the dot and colored red . in addition the word  sbjct ( on the left of the figure ) is also colored red if there is a mismatch on the line . enable this option with the  alignment view pull - down menu shown in figure 3 . the majority of blast searches at the ncbi web site are nucleotide queries against nucleotide databases ( e.g. blastn ) . the standard blast report does not show the amino acid sequence translated from the query or annotated on the database sequence , even though that may be of great interest to the user ; furthermore figuring out the positions of the encoded amino acids on the corresponding nucleotide sequence can be challenging , especially if the coding region is long or involves multiple exons . any pre - annotated cds protein products on the query ( if the query is an accession ) or the database sequence are fetched from entrez and shown with the residues aligned to the second base of a codon ( figure 2 ) . for a user - submitted query in fasta format a putative protein product is calculated using the coding frame of the database sequence as a guide . combined with the  pairwise with identities option discussed above this format makes certain tasks easier , such as analysis for silent and replacement mutations . owing to the overhead of fetching the cds feature from entrez this option is currently not the default . low complexity sequences are compositionally biased regions of amino acid or nucleotide sequence , which often result in artificially high scores in sequence similarity searches . low - complexity filters , such as seg ( 6 ) or dust , mask these regions and prevent them from overly biasing the results . traditionally blast has replaced the masked regions by xs or ns in the blast report . the blast formatter now can represent these regions by lower - case letters , making them distinct from the ( upper - case ) non - filtered regions ( figure 2 ) . in addition the user may select from three colors ( black , gray , red ) to vary the emphasis on these regions ( figure 3 ) . this new display option is now the default , showing the masked regions in gray lower - case . it is useful for quickly localizing regions of interest in the query based on it 's similarity to other sequences in the database . to reduce the complexity in generating this graphic overview we have now implemented it as html tables that use a few small static images ( gifs ) . this design is more robust and also lends itself to future development of a graphical viewer for stand - alone and command - line client blast . this can be essential if the database sequence is long , such as a chromosome , and the alignment to be presented only involves a small fraction of the sequence . previously the entire database sequence was fetched and much of that sequence was not used . this improved functionality has led to a dramatic decrease in formatting time for searches against genomes . the query - anchored view gives a stacked view of database sequences aligned to the query with indication of insertions and mismatches ( 3 ) . this provides an easy method to scan alignments and locate things like snp 's and amino acid substitutions among a group of related sequences . previously the query - anchored views were not fully supported for blastx and tblastx searches that involved translated sequences . use the  alignment view pull - down to enable this option ( figure 3 ) . from the blast results it is now possible to select some or all of the database sequences and perform an entrez query to fetch them . checking the boxes in the alignment section selects the sequences to download and clicking the  get selected sequences button takes the user to entrez , where the sequences can be displayed in various formats , ( such as genbank or fasta ) and saved to a file . we are currently redesigning the blast web pages to make them more effective tools . some of the changes will be better organized html that makes options apparent to the user , such as making it easier to limit a search or results to a particular organism or subset of the data available . nearing completion is a utility to calculate distances between sequences in the blast results and present those as a tree . finally we are also working on making it possible to save search or formatting strategies for future use . during the past five years many genomes have become searchable and the sequences in those databases are typically long contigs or chromosomes . additionally many long nucleotide sequences have been added to the blast databases as a result of high - throughput genomic projects . traditionally sequences in the blast database have been associated with only one descriptive phrase that is normally the same as the  definition in the genbank flat file . this means that only very generic information is provided for matches to long database sequences , even though such a sequence might have annotations for many genes , coding regions ( cds ) and other features . the top line of figure 1 shows a database sequence definition and merely states that the sequence is part of human chromosome 6 and is about 48 million bases long . this reveals little about the region of the database sequence containing the match . to address this issue , we now provide feature information for blast alignments involving long database sequences ( currently defined as larger than 200 kb ) . two types of sequence features ( cds and rrna ) are currently supported but this could be expanded to other features . an example is shown in figure 1 where a custom definition line is displayed for each of the two alignments . according to the custom definition lines the query matches a region inside the human major histocompatability complex ( mhc ) a gene , as well as a region that is about 54 kb upstream of the mhc a gene and about 58 kb downstream of the mhc g gene , allowing one to quickly draw the conclusion that the query sequence is highly related to the human mhc . frequently alignments are between very similar sequences and it 's difficult to identify a few mismatches in the pairwise alignment . to address this issue we recently introduced a new format called  pairwise with identities , shown in figure 2 on an alignment with 98% identity between the query and database sequence . a dot indicates identity between the database sequence and query at that position ; mismatches are shown as the database sequence letter in place of the dot and colored red . in addition the word  sbjct ( on the left of the figure ) is also colored red if there is a mismatch on the line . enable this option with the  alignment view pull - down menu shown in figure 3 . the majority of blast searches at the ncbi web site are nucleotide queries against nucleotide databases ( e.g. blastn ) . the standard blast report does not show the amino acid sequence translated from the query or annotated on the database sequence , even though that may be of great interest to the user ; furthermore figuring out the positions of the encoded amino acids on the corresponding nucleotide sequence can be challenging , especially if the coding region is long or involves multiple exons . any pre - annotated cds protein products on the query ( if the query is an accession ) or the database sequence are fetched from entrez and shown with the residues aligned to the second base of a codon ( figure 2 ) . for a user - submitted query in fasta format a putative protein product is calculated using the coding frame of the database sequence as a guide . combined with the  pairwise with identities option discussed above this format makes certain tasks easier , such as analysis for silent and replacement mutations . owing to the overhead of fetching the cds feature from entrez this option is currently not the default . low complexity sequences are compositionally biased regions of amino acid or nucleotide sequence , which often result in artificially high scores in sequence similarity searches . low - complexity filters , such as seg ( 6 ) or dust , mask these regions and prevent them from overly biasing the results . traditionally blast has replaced the masked regions by xs or ns in the blast report . the blast formatter now can represent these regions by lower - case letters , making them distinct from the ( upper - case ) non - filtered regions ( figure 2 ) . in addition the user may select from three colors ( black , gray , red ) to vary the emphasis on these regions ( figure 3 ) . this new display option is now the default , showing the masked regions in gray lower - case . it is useful for quickly localizing regions of interest in the query based on it 's similarity to other sequences in the database . to reduce the complexity in generating this graphic overview we have now implemented it as html tables that use a few small static images ( gifs ) . this design is more robust and also lends itself to future development of a graphical viewer for stand - alone and command - line client blast . this can be essential if the database sequence is long , such as a chromosome , and the alignment to be presented only involves a small fraction of the sequence . previously the entire database sequence was fetched and much of that sequence was not used . this improved functionality has led to a dramatic decrease in formatting time for searches against genomes . the query - anchored view gives a stacked view of database sequences aligned to the query with indication of insertions and mismatches ( 3 ) . this provides an easy method to scan alignments and locate things like snp 's and amino acid substitutions among a group of related sequences . previously the query - anchored views were not fully supported for blastx and tblastx searches that involved translated sequences . use the  alignment view pull - down to enable this option ( figure 3 ) . from the blast results it is now possible to select some or all of the database sequences and perform an entrez query to fetch them . checking the boxes in the alignment section selects the sequences to download and clicking the  get selected sequences button takes the user to entrez , where the sequences can be displayed in various formats , ( such as genbank or fasta ) and saved to a file . we are currently redesigning the blast web pages to make them more effective tools . some of the changes will be better organized html that makes options apparent to the user , such as making it easier to limit a search or results to a particular organism or subset of the data available . nearing completion is a utility to calculate distances between sequences in the blast results and present those as a tree . finally we are also working on making it possible to save search or formatting strategies for future use . the query was bases 241 through 480 of a human mhc a gene nucleotide sequence ( nm_002116 ) in a search against the human genome . custom definition lines are provided for both of the alignments shown and are relevant to the region matched ( first alignment ) or nearby regions ( second alignment ) . fasta sequence for the human cystic fibrosis trans - membrane conductance regulator sequence ( nm_000492 ) was used as query for a blastn search against the nr database using default parameters . nucleotide matches in the database sequence are shown as dots (  . ) , nucleotide mismatches in the database sequence ( as well as the database sequence identification ) are colored red . the second new option is the presentation of the cds features , which is shown for both the query and database sequences above and below the blast alignment , respectively . the cds feature annotated on the database sequence was retrieved from entrez ; the putative cds feature on the query was produced automatically using the cds of the database sequence as a guide . mismatches for the amino acid sequence derived from the database sequence are colored pink . finally the new masking option is shown ( see text ) . bases 175181 of the query were masked for low - complexity during the search and are shown in lower - case gray letters . the red arrows point to new report features that may be enabled or modified from this page . the check - box highlighted by arrow 1 enables the cds feature on a blastn or megablast search . the two menus highlighted by arrow 2 change the default behavior for display of masked regions . the menu highlighted by arrow 3 changes how the alignments are displayed in the blast report .
basic local alignment search tool ( blast ) is a sequence similarity search program . 
 the national center for biotechnology information ( ncbi ) maintains a blast server with a home page at . 
 we report here on recent enhancements to the results produced by the blast server at the ncbi . these include features to highlight mismatches between similar sequences , 
 show where the query was masked for low - complexity sequence , and integrate information about the database sequences from the ncbi entrez system into the blast display . 
 changes to how the database sequences are fetched have also improved the speed of the report generator .