---
title: "blast - Basic Local Sequence Alignments"
canonical: "https://help.biobam.com/space/DOC/694877/blast%20-%20Basic%20Local%20Sequence%20Alignments"
format: markdown
---
> Macro (toc)

## Run BLAST at the NCBI

<span style="color: #222222">Here, the user can specify the following parameters, which are divided into three different sections: Blast Configuration in Figure 2, Advanced in Figure 3</span> <span style="color: #222222">and Save Results Page Figure 4</span>

### Blast Configuration Page

- Your e-mail address in case you are using the NCBI BLAST web service.
- BLAST program: The algorithm you want to use:
  - blastp - Compares an amino acid query sequence against a protein sequence database.
  - blastn (-task blastn) - Compares a nucleotide query sequence against a nucleotide sequence database.
  - blastx - Compares a nucleotide query sequence translated in all reading frames against a protein sequence database. Used to find potential translation products of an unknown nucleotide sequence
  - tblastn - Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.
  - blastx-fast
  - blastp-fast
  - blastp-short
  - blastn (-task megablast)
  - blastn (-task dc-megablast)
  - blastn-short
  - tblastn-fast
- BLAST DB: The name of the database to search in (eg. nr, swissprot, pdb). To see a list of possible DBs at NCBI seehttp://data.biobam.com/ncbi_blast_dbs_protein.pdf
- Taxonomy Filter: Search for Blast results only in the selected taxonomy.
- BLAST expect value: The statistical significance threshold for reporting matches against database sequences. If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Increasing the threshold shows less stringent matches.
- Number of BLAST hits: The number of alignments you want to achieve (0-100).

BLAST Description Annotator: The BDA finds the best possible description for a new sequence based on a given BLAST result.

> Macro (anchor)



### Advanced Page (PRO Feature)

- Blast Parameters:
  - Word size: One of the important parameters governing the sensitivity of BLAST searches is the length of the initial words. The word size is adjustable in blastn and can be reduced from the default value to increase sensitivity. This word size can also be increased to increase the search speed and limit the number of database hits.
  - Low complexity filter: The BLAST programs employ the SEG algorithm to filter low complexity regions from proteins before executing a database search. Default is ON.
- Filter Options:
  - HSP length cutoff: A Cutoff value for the minimal length of the first hsp of a blast hit, used to exclude hits with only small local alignments from the BLAST result. The given length corresponds to amino acids or nucleotides depending on the type of performed BLAST.
  - HSP-Hit Coverage
  - Filter by description: Filter-out Blast hits by description

> Macro (anchor)



### Save Results Page

<span style="color: #222222">The results of the BLAST queries can also be directly saved to a file in different formats by selecting the corresponding check boxes at the BLAST Save Results Page. If the chosen file already exists, upcoming results will be appended. Choose a format type to additionally save your BLAST results.</span>

- XML2: This is a new BLAST results provided by NCBI and can also be loaded into Blast2GO.
- XML: It is recommended to save your BLAST results as XML as this format is supported by the Blast2GO Load BLAST Results function.
- TXT: It saves the blast results of each sequence in text file format.
- HTML: For each sequence a file in htlm format will be saved.



  


- E-Value Distribution: This chart plots the distribution of E-values for all selected BLAST hits. It is useful to evaluate the success of the alignment for a given sequence database and help to adjust the E-Value cutoff in the annotation step.
- Similarity Distribution: This chart displays the distribution of all calculated sequence similarities (percentages), shows the overall performance of the alignments and helps to adjust the annotation score in the annotation step.
- Species Distribution: This chart gives a listing of the different species to which most sequences were aligned during the BLAST step.
- Top-Hit Species Distribution: Bar chart showing the species distribution of all Top-Blast hits.
- Hit Distribution: This chart shows a distribution of the number of hits for the blasted sequences in a data-set.
- Hsp Distribution: This bar chart shows the distribution of hsps per hit.
- Hsp/Seq Distribution: This chart shows a distribution of percentages that represents the coverage between the hsps and their corresponding sequences.
- Hsp/Hit Distribution: Same as above but for hits instead of sequences


## Other BLAST Functions

- Remove Blast Results: This option will remove the BLAST results from the selected sequences.
- Run Blast-Descriptor-Annotator (BDA): This will run the BDA algorithm. For further details, please see [Blast Configuration Page](/wiki/pages/resumedraft.action?draftId=694877#BLAST-BlastConfigurationPage) section.
- Recover original Best-Blast-Hit Description: When this option is executed the sequence description column on the Main Sequence Table will contain the top blast hit description and not the one from the BDA.