Result Format Options¶
An overview of the database sequences aligned to the query sequence is shown. The score of each alignment is indicated by one of five different colors, which divides the range of scores into five groups. Multiple segments of alignments to the same database sequence are connected by a thin grey line. Mousing over a hit sequence causes the definition and score to be shown in the window at the top, clicking on a hit sequence takes the user to the associated alignments.
Checking this option will allow BLAST formatter to parse out the annotated sequence features found in or around the vicinity of hits and display them within the BLAST result. For custom query sequences, it will also translate the CDS using the CDS translation annotated on matching database sequence as a guide. Mismatch in translation will be highlighted in pink. A representative example with CDS translation is given below.
gi|46452254|gb|AY585334.1| Sus scrofa cystic fibrosis transmembrane conductance regulator (CFTR) mRNA, complete cds Length=4449 Score = 5453 bits (2751), Expect = 0.0 Identities = 4036/4449 (90%), Gaps = 6/4449 (0%) Strand=Plus/Plus CDS: Putative 1 1 M Q R S P L E K A S V V S K L F F S W T Query 133 ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCGTTGTCTCCAAACnnnnnnnCAGCTGGACC 192 |||||||||||||||||||||||||||||| | |||||||||||||||||||||||||| Sbjct 1 ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCATCTTCTCCAAACTTTTTTTCAGCTGGACC 60 CDS:cystic fibrosis 1 M Q R S P L E K A S I F S K L F F S W T CDS: Putative 1 21 R P I L R K G Y R Q R L E L S D I Y Q I Query 193 AGACCAATTTTGAGGAAAGGATACAGACAGCGCCTGGAATTGTCAGACATATACCAAATC 252 |||||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||| Sbjct 61 AGACCAATTTTGAGAAAAGGATATAGACAGCGCCTGGAATTGTCAGACATATACCATATC 120 CDS:cystic fibrosis 21 R P I L R K G Y R Q R L E L S D I Y H I CDS: Putative 1 41 P S V D S A D N L S E K L E R E W D R E Query 253 CCTTCTGTTGATTCTGCTGACAATCTATCTGAAAAATTGGAAAGAGAATGGGATAGAGAG 312 ||||| ||| |||||||||||||| |||||||||||||||||||||||||| ||||| Sbjct 121 TCTTCTTCTGACTCTGCTGACAATCTGTCTGAAAAATTGGAAAGAGAATGGGACAGAGAA 180 CDS:cystic fibrosis 41 S S S D S A D N L S E K L E R E W D R E
There are two options that determines the way filter masked region should be displayed in.
X or N displays the masked region in X for protein and N for nucleotide.
Lower Case displays maksed region in lower case letters.
The masked region can be “highlighted” with grey or red colored fonts.
This option restricts the number of short descriptions of matching sequences reported to the number specified. Default setting varies from page to page. See also expect.
The databases alignments are displayed as pairs of matches between query and subject sequence. A middle line between the query and subject sequence displays the status of a letter. For protein alignments (e.g, BLASTP/BLASTX/TBLASTN), identities present the letter, conservative substitutions present a “+”, and nothing otherwise. For nucleotide alignments (e.g., BLASTN and megaBLAST) a “|” is shown for matches and nothing for mismatches. This is the default view.
Pairwise with dots for identities
The databases alignments are anchored (shown in relation to) to the query sequence in pairwised fashion with mismatches colored in red. Sbjct will be in red and bold font if a line in the alignment contains mismatches. See example below.
Query-anchored with dots for identities
Identities are displayed as dots (.), with mismatches displayed as single letter abbreviations.
Query-anchored with letters for identities
Identities are shown as single letter nucleotide abbreviations.
Flat Query-anchored with dots for identities
The ‘flat’ display shows inserts as deletions on the query. Identities are displayed as dots (.), with mismatches displayed as single letter abbreviations.
Flat Query-anchored with letters for identities
The ‘flat’ display shows inserts as deletions on the query. Identities are shown as single letter abbreviations.
gi|21536448|ref|NM_002622.3| Homo sapiens prefoldin 1 (PFDN1), mRNA Length=1296 Score = 392 bits (212), Expect = 2e-107 Identities = 220/223 (98%), Gaps = 3/223 (1%) Strand=Plus/Plus Query 107 TCCTACCTGGAGCGAAG-GTTANAGGAAGCTGAGGACAACATCCGGGAGATGCTGATGGC 165 Sbjct 300 ................. C .... - ..................................... 358 Query 166 ACGAAGGG-CCAGTAGGGAGCCTCTCTGGGAAGCTCTTCCTCCTGCCCCTCCCATTCCTG 224 Sbjct 359 ........ C ................................................... 418 Query 225 GTGGGGGCAGAGGAGTGTCTGCAGGGAAACAGCTTCTCCTCTGCCCCGATGGATGCTTTA 284 Sbjct 419 ............................................................ 478 Query 285 TTTGGATGGCCTGGCAACATCACATTTTCTGCATCACCCTGAG 327 Sbjct 479 ........................................... 521
The Download links allows downloads of XML, Text report, CSV, XML, ASN.1 or JSON.
Format for PSI-BLAST¶
The Position-Specific Iterated BLAST (PSI-BLAST) program performs iterative searches with a protein query, in which sequences found in one round of search are used to build a custom score model for the next round.
In PSI-BLAST the algorithm is not tied to a specific score matrix, such as BLOSUM62, which has been implemented using an AxA substitution matrix where A is the alphabet size. Instead, it uses a QxA matrix, where Q is the length of the query sequence. At each position the cost of a letter depends on the position with regard to the query and the letter in the subject sequence.
To run this search, “Format for PSI-BLAST” checkbox must be checked.
This sets the statistical significance threshold for including a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.
Limit results by entrez query¶
This function is similar to the “Limit by Entrez Query terms” in the option section. The only difference is that it applies only to the identified hits. In another word, it is applied post-search and allows users to see only hits fitting the requirement of the Entrez query terms. Default is to format without input query terms and allow users to see all the hits.
Expect value range¶
This instructs BLAST formatter to display hits with Expect value within the specified range. Default value is 0 to Expect value setting. Lower bound goes to the first box, higher bound goes to the second box.