Search FlyBase sequences with NCBI BLAST+ 2.17.0. Choose the program that matches your query and the database you want to search.
For the full program and parameter reference, see the NCBI BLAST+ User Manual. The NCBI BLAST Help guide also explains search concepts and results.
Choose a program
| Program | Your query | Searches | How it compares sequences |
|---|---|---|---|
| blastn | Nucleotide | Nucleotide database | Compares DNA or RNA sequences directly. |
| blastp | Protein | Protein database | Compares amino acid sequences directly. |
| blastx | Nucleotide | Protein database | Translates your query into protein sequences. |
| tblastn | Protein | Nucleotide database | Translates the database sequences into proteins. |
| tblastx | Nucleotide | Nucleotide database | Translates both your query and the database sequences. |
Prepare your query
- Paste a sequence or upload a FASTA file, up to 1 MiB and 100 records. If both are supplied, the pasted sequence is used.
- For multiple FASTA records, give each sequence a header beginning with
>. Each record has its own results; use the query selector to move between them. - Use protein input for blastp and tblastn, and nucleotide input for the other programs.
- Check the database information for the sequence releases available. The database release used is also recorded with your results.
Adjust your search
- Expect (E value)
- The expected number of matches of similar quality that could occur by chance. Lower values are more stringent.
- Low-complexity filtering
- Masks repetitive or compositionally biased query regions that can produce uninformative matches.
- Word size
- Controls the initial match size. Smaller words can improve sensitivity but may take longer to search.
- MegaBLAST
- A nucleotide search option suited to highly similar sequences.
- Matrix and genetic code
- The scoring matrix applies to protein comparisons. The genetic code controls translation of nucleotide sequences.
Additional options for experienced users
The Additional options field accepts these legacy-style flags where supported by the selected program. FlyBase translates them to BLAST+ parameters.
-G: gap opening cost;-E: gap extension cost.-q: nucleotide mismatch penalty;-r: nucleotide match reward.-y: ungapped X-drop;-X: gapped X-drop;-Z: final gapped X-drop.
See the NCBI manual for parameter details. Unsupported options produce a validation message.
Read and keep your results
- A search may briefly queue before it runs. Keep the result page open to follow its progress.
- Results are available in the same browser session for 72 hours. Download anything you want to keep longer.
- Click a match in the graphical overview or select View alignments in the hit summary to jump to its alignment.
- Descriptions and Alignments control how much is displayed. Search archives retain up to 500 matching subjects. The overview shows up to 20 aligned segments (HSPs) per hit; longer alignment lists use pagination.
- Use the Text, Tabular, XML or ASN downloads to save the recorded search results.
Searches that exceed 600 seconds or the available resources stop with an error message. If that happens, try a shorter query or a more specific database.
Need help?
Use Contact FlyBase at the bottom of the page. Include the program, database, and any error message so we can help you troubleshoot.