Result Format Options

Graphical Overview

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.

CDS feature

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

Masking

There are two options that determines the way filter masked region should be displayed in.

  • Masking Character

    • X or N displays the masked region in X for protein and N for nucleotide.

    • Lower Case displays maksed region in lower case letters.

  • Masking Color

    The masked region can be “highlighted” with grey or red colored fonts.

Descriptions

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.

Alignment View

  • Pairwise

    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

Download

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.

Inclusion Threshold

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.