Downloading fasta files from genban

Select the file format. Choose the delimiter characters that will separate the qualifiers from one another in the header line.

Select whether to extract translated amino acid sequences, DNA sequence for each feature, or the entire DNA sequence of the whole record. To choose how your header line appears, designate the names of the qualifiers, one per field, in the order that you want them to appear in the FASTA header line. Common feature and qualifier choices are already filled in, but you may put your own choices in their place.

A description of potential feature keys and qualifiers can be found here. A stand alone command line version of this software is available here. Please only process one file at a time, so as not to overload our server. If your input file is more than a few MB, please download the stand alone version. Input your file: Please select a file to convert. File name must have no spaces, or odd characters. Support for EMBL files is experimental.

Amino Acid sequence translated on the fly Generates a translation from the nucleotide sequence on the fly based on the position. Takes into account joins, in other words introns are excluded from exported sequences. Does not take into account RNA editing. Also, where fuzzy locations are given, we just pick a spot. Sorry, I can't post a comment with my reputation score. However, your command is downloading all sequences from the input file into a single fasta file. I believe that if you have a big bunch of sequences, it could be a little bit tricky after to manipulate that kind of file.

Just by curiosity, do you have a trick to create one sequence per file using efetch? Sign up to join this community. The best answers are voted up and rise to the top. Stack Overflow for Teams — Collaborate and share knowledge with a private group. Create a free Team What is Teams? Learn more. Ask Question. Asked 2 years, 1 month ago. Active 1 year, 9 months ago. Viewed 9k times. Improve this question. Add a comment. Active Oldest Votes.

Improve this answer. Matteo Ferla Matteo Ferla 2, 3 3 silver badges 16 16 bronze badges. Downloading a few sequences For this, you can use Entrez Direct as mentioned by dc BlueSky BlueSky 2 2 bronze badges.

Whether you want a large number of files or just one file is, I guess, a personal choice. A multifasta file is fairly standard though. I don't think you can create individual files for each sequence using epost and efetch ; you will have to either use a bash script or postprocess the efetch output using the unix tool split.