Tutorial Cara Melakukan BLAST NCBI (Basic Local Alignment Search Tool)

Summary

This video explains how to use the BLAST (Basic Local Alignment Search Tool) program to compare nucleotide sequences against a database to identify genes or species. The process involves inputting a DNA sequence or uploading a file in FASTA format to the BLAST website, selecting nucleotide BLAST, and analyzing the results to find similar sequences. The tutorial guides users through the steps of performing a BLAST search, interpreting the results, and understanding the significance of alignment values. It also explores how to compare sequences, download results, and generate phylogenetic trees based on sequence similarities.

Takeaways

• 😀 The video introduces the concept of BLAST (Basic Local Alignment Search Tool), a program used to search DNA or protein sequences against a database to find similar sequences.
• 😀 BLAST helps in identifying the species or gene from a DNA sample by comparing it with known sequences in a database.
• 😀 The video demonstrates how to use the NCBI BLAST website to perform nucleotide-based sequence searches.
• 😀 To use BLAST, users can either copy the sequence directly or upload a FASTA file containing the sequence they want to search.
• 😀 The NCBI BLAST website offers multiple types of BLAST searches, including nucleotide, protein, and translated nucleotide sequences.
• 😀 The video explains how to use the NCBI website to search for human actin gene sequences and the results that can be obtained.
• 😀 Sequence alignment results show how closely related a user’s sequence is to database sequences based on alignment and similarity.
• 😀 The I-value (e-value) of BLAST results indicates the significance of the alignment; a lower e-value suggests a higher similarity and relevance.
• 😀 The results of a BLAST search are displayed with a color-coded alignment indicating the degree of similarity between sequences.
• 😀 The video also discusses how to download and save BLAST results in FASTA format for further analysis and how to interpret the results for sequence comparisons.
• 😀 Users can select specific results from the BLAST output and download the sequences or even view the taxonomic relationships of the aligned sequences.

Q & A

What is the purpose of performing a BLAST search?

A BLAST search is used to compare a given nucleotide or protein sequence against a database to find sequences that are similar or related. It helps identify genes, determine their origin, and explore relationships between species or genes.

How can you input your nucleotide sequence into BLAST for comparison?

You can input your nucleotide sequence into BLAST by either copying and pasting the sequence directly into the provided query box or by uploading a file containing the sequence.

What does the term 'BLAST' stand for?

BLAST stands for Basic Local Alignment Search Tool, a program used to compare nucleotide or protein sequences against a database to find similar sequences.

What options are available on the BLAST website for performing a search?

The BLAST website offers several search options, including nucleotide BLAST, protein BLAST, and searches for translated nucleotide sequences against protein databases, or vice versa.

How do you obtain a FASTA format for a sequence to use in BLAST?

You can obtain a FASTA format by either copying the sequence from a database or directly exporting it in FASTA format from a resource like GenBank.

What does the E-value indicate in BLAST results?

The E-value in BLAST results reflects the statistical significance of the match. A smaller E-value indicates a higher probability that the sequences are related, meaning the match is more likely to be meaningful.

What is the purpose of viewing sequence alignment in BLAST results?

Viewing the sequence alignment allows you to compare your query sequence with sequences from the database, showing how closely they match at the nucleotide level and highlighting any mismatches or gaps.

What is the significance of gaps in sequence alignments during BLAST?

Gaps in sequence alignments occur when one sequence has bases or amino acids that are missing from the other. This may indicate differences in gene structure or evolutionary changes.

How do you interpret the color coding in BLAST alignment results?

In BLAST results, the color coding indicates the degree of similarity. Red represents high similarity, while other colors, such as green or purple, indicate decreasing similarity or gaps in alignment.

What is a taxonomy tree in BLAST results, and what does it represent?

A taxonomy tree in BLAST results visually represents the evolutionary relationships between the sequences you are comparing. It shows how closely related different species are based on sequence similarity.