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# Basic Local Alignment Search Tool

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- Message ID#29 Error: Query string not found in the CGI context

Query
Database
  nr
Job title
Entrez Query
  Note: Your search is limited to records matching this Entrez query
Request ID
  Show results in a new window
Format

  Show

  as
  Old View Reset form to defaults [?]

  These options control formatting of alignments in results pages. The default is HTML, but other formats (including plain text) are available. PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST. The Advanced view option allows the database descriptions to be sorted by various indices in a table. more...

  Alignment View | [?] Choose how to view alignments. The default "pairwise" view shows how each subject sequence aligns individually to the query sequence. The "query-anchored" view shows how all subject sequences align to the query sequence. For each view type, you can choose to show "identities" (matching residues) as letters or dots. more...

  Display

  Graphical Overview Linkout Sequence Retrieval NCBI-gi CDS feature [?]
  - Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to query. more...
  - Database LinkOuts: Show links from matching sequences to entries in specialized NCBI databases. more...
  - Sequence Retrieval: Show buttons to download matching sequences. more...
  - NCBI-gi: Show NCBI gi identifiers. more...
  - CDS feature: Show annotated coding region and translation. more...

  Masking

  Character:
  Color:
  [?]
  - Masking Character: Display masked (filtered) sequence regions as lower-case or as specific letters (N for nucleotide, P for protein).
  - Masking Color: Display masked sequence regions in the given color.

  Limit results

  Descriptions:
  Graphical overview:
  Alignments:
  Line length:
  [?]
  - Descriptions: Show short descriptions for up to the given number of sequences.
  - Alignments: Show alignments for up to the given number of sequences, in order of statistical significance.
  - Line lenghth: ....

  | Organism Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown. Exclude [?] Show only sequences from the given organism.
  | Entrez query: [?] Show only those sequences that match the given Entrez query. more...
  | Expect Min: Expect Max: [?] Show only sequences with expect values in the given range. more...
  | Percent Identity Min: Percent Identity Max: [?] Show only sequences with percent identity values in the given range.

  Format for

  PSI-BLAST with inclusion threshold: [?]
  - 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. more...
  - 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.