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BLAST Feature

This feature uses a powerful bioinformatics tool used to compare a query sequence (DNA, RNA, or protein) against a database of sequences to identify regions of similarity. The tool offers various types of BLAST searches, including:
  • blastn: for nucleotide-nucleotide comparisons
  • blastp: for protein-protein comparisons
  • blastx: for nucleotide query against protein database
  • tblastn: for protein query against nucleotide database
For example:
Prompt
search blastp for MKVKVLSLLVPALLVAGAANAAEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF and save the result
Response
Certainly! I'll use the search_blast tool to perform a BLASTP search for the protein sequence you provided. I'll set the tool to save the results as well.

The BLAST search results for the provided protein sequence reveal several important findings:
1.	Sequence Identity: The query sequence shows high similarity (88–88% identity) to multiple porin OmpF proteins, primarily from Escherichia coli strains.
2.	Top Hits: The top hits include:
- WP_077492852.1 porin OmpF [Escherichia coli] with a score of 630 bits and 88% identity
- MBS8794624.1 porin OmpF [Escherichia coli] with a score of 629 bits and 88% identity
- AFA1190.1 outer membrane protein F [Escherichia coli] with a score of 629 bits and 88% identity
3.	Protein Function: The results confirm that the query sequence is a porin OmpF, an outer membrane protein that forms water-filled channels allowing passive diffusion of small hydrophilic molecules across the outer membrane.
4.	Conservation: The high sequence similarity across various E. coli strains suggests that this protein is highly conserved, indicating its crucial role in cellular function.
5.	Taxonomic Distribution: While most hits are from E. coli, there are also matches from other Enterobacteriaceae, including Shigella flexneri, suggesting a broader distribution within this bacterial family.
6.	Structural Implications: The high conservation suggests that the protein's structure, including its beta-barrel formation and channel properties, is likely preserved across these bacterial strains.
7.	E-value: All top hits have an E-value of 0.0, indicating extremely high statistical significance of the matches.
8.	Alignment Details: The alignments show very few gaps, mostly concentrated in one region (positions 52–60 of the query sequence), suggesting a possible insertion/deletion event in this area.
9.	Database Information: The search was conducted against a comprehensive database including 829,996,675 sequences, ensuring a wide coverage.

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Scientific Notations

I fully support scientific notations in KaTeX format. Here is an example of question a Math teacher asked:
Prompt
Evaluate the triple integral of f(x,y,z) = z, where z goes from 0 to sqrt(4-x^2-y^2), and y goes from -sqrt(4-x^2) to sqrt(4-x^2) and x goes from -2 to 2
Response
Prompt
If 20.86 mL of 2.29 M potassium iodide is needed to reach the equivalence point with 16.29 mL of lead (II) nitrate, determine the molarity of the lead (II) nitrate solution.
Note: First write the balance equation between potassium iodide and lead (II) nitrate.
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