Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi and follow the links to nucleotide BLAST. Type in the sequence below; it is broken up into codons to make it easier to copy.
5' ATG TTC GTC AAT CAG CAC CTT TGT GGT TCT CAC CTC GTT GAA GCTTTG TAC CTT GTT TGC GGT GAA CGT GGT TTC TTC TAC ACT CCT AAG ACT TAA 3'
As you will note on the BLAST page, there are several options for tailoring your query to obtain the most relevant information. Some are related to which sequences to search in the database. For example, the search can be limited taxonomically (e.g., restricted to mammals) or by the type of sequences in the database (e.g., cDNA or genomic). For our search, we will use the broadest database, the 'Nucleotide collection (nr/nt).' This is the nonredundant (nr) database of all nucleotide data (nt) in GenBank and can be selected in the 'Database' dialogue box. Other parameters can also be adjusted to make the search more or less sensitive to mismatches or gaps. For our purposes, we will use the default setting, which is automatically presented. Press 'BLAST' to search. What can you say about the DNA sequence?

Verified step by step guidance

1. Step 1: Understand the purpose of the BLAST search. BLAST (Basic Local Alignment Search Tool) compares your input DNA sequence against a large database of known sequences to find regions of similarity, which can help identify the gene or organism your sequence might come from.
2. Step 2: Prepare the sequence for input. The sequence is given in codons (groups of three nucleotides) from 5' to 3'. When entering it into the BLAST search box, remove spaces and line breaks so the sequence is continuous, for example: 5'-ATGTTCGTCAATCAGCACCTTTGTGGTCTCACC...-3'.
3. Step 3: Select the appropriate database. Choose the 'Nucleotide collection (nr/nt)' database, which is a comprehensive, nonredundant collection of nucleotide sequences from GenBank. This ensures your query is compared against a broad range of sequences.
4. Step 4: Use default BLAST parameters. The default settings balance sensitivity and speed, allowing for mismatches and gaps to find the best alignments without being too restrictive or too permissive.
5. Step 5: Interpret the BLAST results. After running the search, examine the top hits to see which known sequences closely match your query. Look at the organism names, gene annotations, and alignment scores to infer the identity or function of your DNA sequence.

Key Concepts

BLAST (Basic Local Alignment Search Tool)

BLAST is a bioinformatics tool used to compare a query DNA or protein sequence against a database to find regions of similarity. It helps identify homologous sequences, infer functional and evolutionary relationships, and annotate genes. The nucleotide BLAST specifically compares DNA sequences to nucleotide databases.

Nucleotide Sequence Databases and Search Parameters

Nucleotide databases like GenBank contain vast collections of DNA sequences from various organisms. Selecting the appropriate database and search parameters (e.g., taxonomic limits, sequence type) affects the relevance and sensitivity of BLAST results, enabling targeted or broad searches depending on research goals.

Interpreting BLAST Results

BLAST results provide alignments showing sequence similarity, including scores, E-values, and identities. Understanding these metrics helps determine if the query sequence matches known genes or organisms, revealing potential function or origin. High similarity and low E-values indicate significant matches.