Hi, everyone
I would like to know if there is there any bioinformatic tool that can download batch DNA seq using imported NCBI accession numbers (upto 100 sequences) and translate them into multiple aa seqs?
Thank you for your answer in advance
Please visit BatchEntrez, NCBI to download sequences and translate in to AA seq as well.
Yes, there are several bioinformatic tools and scripts that can help you download batch DNA sequences using NCBI accession numbers and translate them into amino acid sequences. Below are a few methods and tools you can use:
1. NCBI E-utilities and BioPython
BioPython is a powerful library for biological computation. It includes modules to interact with NCBI, download sequences, and perform translations.
Example Python Script:
pythonCopy codefrom Bio import Entrez, SeqIO # Function to download DNA sequences from NCBI def fetch_sequences(accession_numbers): Entrez.email = "[email protected]" # Always provide your email handle = Entrez.efetch(db="nucleotide", id=accession_numbers, rettype="fasta", retmode="text") records = list(SeqIO.parse(handle, "fasta")) handle.close() return records # Function to translate DNA sequences to amino acid sequences def translate_sequences(dna_sequences): aa_sequences = [] for record in dna_sequences: aa_sequences.append(record.seq.translate()) return aa_sequences # List of NCBI accession numbers accession_numbers = ["NM_001200025", "NM_001354563", "NM_001368233"] # Example accession numbers # Fetch and translate sequences dna_sequences = fetch_sequences(accession_numbers) aa_sequences = translate_sequences(dna_sequences) # Print amino acid sequences for aa_seq in aa_sequences: print(aa_seq)
2. NCBI Batch Entrez
NCBI Batch Entrez allows users to download sequences in bulk by entering a list of accession numbers. You can download the sequences in FASTA format and then use a script to translate them.
3. Command-line Tools: EMBOSS
The European Molecular Biology Open Software Suite (EMBOSS) provides command-line tools for sequence analysis, including translation.
Example Commands:
bashCopy code# Download sequences using NCBI Entrez (using Entrez Direct) esearch -db nucleotide -query "NC_000001.11 OR NC_000002.12" | efetch -format fasta > sequences.fasta # Translate DNA sequences to amino acid sequences transeq -sequence sequences.fasta -outseq aa_sequences.fasta
4. Galaxy Platform
Galaxy is an open, web-based platform for data-intensive biomedical research. It provides tools for sequence retrieval and translation.
Steps:
5. Online Tools
Several online tools allow you to input a list of accession numbers, download the sequences, and translate them.
Example:
- SequenceServer – This can be used for batch sequence retrieval.
- ExPASy Translate Tool – For translating DNA sequences into amino acid sequences.
By using these tools and methods, you can efficiently download and translate multiple DNA sequences using NCBI accession numbers. If you need any further assistance or more detailed guidance, feel free to ask!
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