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formatting tweak
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shiltemann committed Jan 14, 2025
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Expand Up @@ -259,13 +259,12 @@ Tabular-to-FASTA is a tool used to convert tabular data into the FASTA format, c
In this step, the NCBI BLAST+ blastp tool is used for performing protein sequence alignment. It compares the query protein sequence (generated from the Tabular-to-FASTA tool) against a locally installed BLAST database of protein sequences. The alignment is optimized for shorter protein queries (less than 30 residues) using the blastp-short option. The tool uses a PAM30 scoring matrix, along with specific gap costs, and generates tabular output with extended 25 columns, allowing users to examine the results in detail.
**Parameters:**
- Protein query sequence(s): The input protein sequence in FASTA format.
- Subject database/sequences: The BLAST database against which the query sequence will be compared.
- Type of BLAST: Optimized for short protein queries.
- Expectation value cutoff: Specifies the cutoff for statistical significance.
- Advanced options: Includes scoring matrix (PAM30), gap costs, and word size for the BLAST algorithm.
- **Parameters:**
- **Protein query sequence(s):** The input protein sequence in FASTA format.
- **Subject database/sequences:** The BLAST database against which the query sequence will be compared.
- **Type of BLAST:** Optimized for short protein queries.
- **Expectation value cutoff:** Specifies the cutoff for statistical significance.
- **Advanced options:** Includes scoring matrix (PAM30), gap costs, and word size for the BLAST algorithm.
> <hands-on-title> NCBI BLAST+ blastp </hands-on-title>
>
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