Multi fasta file

If you think it is worth sharing then the comment box is all yours. Hello Nice code. But can you tell if i input multiple keyword form a out file.. Looking forward fro your code. Coming to your nice question. I am sure there will be many better ways to do this task. For example: Lets say, We have a one file, keywords.

Hi Amol! I tried your code with small amount of sequences and keywords, it works well. I am not sure if I used it right or it needs rigid forms of inputs. What about if it is required to extract all sequences from multi-fasta file and keep the name? I found similar code which separate sequences based on regular expression match and then write it to a file numbered sequentially:.

I would like to have similar code but to keep original name of the sequence from multi-fasta not to write it to a files numbered sequentially. It also allows compressing or otherwise processing each extracted file during unpacking. Suppose we have a set of related genomes, for example, 1, genomes of Helicobacter pylori. Uncompressed they occupy 2.

Compressed one by one using gzip results in a MB set of files. A better compressor, such as naf , brings the size down to MB. However, the genomes still remain in 1, separate files.

Let's try the two most common ways of bundling the files together - zip and tar. Although we now have single file, convenient for sharing or moving around, the size is still large. Also, accessing the sequence data now requires de-constructing the archive back into individual files.

A stronger compressor may be able to compress the tar file into a smaller archive. But the necessity to restore the original files before working on them will remain.

We obtain a file that is only 80 MB - 10 times smaller and easy to send over network. This means that many analyses can be performed without unpacking the archive, and without storing 1, files on filesystem. Compressing: mumu. Decompressing and unpacking: unnaf 'Hp.

Suppose you have a set of genomes which are already compressed one by one e. Now you'd like to pack them together and compress them into a single file. The simplest way is to decompress the genomes first, but then you'd have to store all the huge decompressed data.

Ideally you would prefer decompression to occur on-the-fly when packing the sequences together. Using the --cmd option this can be achieved in a single step:. It is also possible to unpack the resulting archive back directly into individually compressed genomes:.

David J. Lipman, William R. Pearson "Rapid and sensitive protein similarity searches" Science , 22 March , , William R. Pearson, David J. Lipman "Improved tools for biological sequence comparison" Proc. USA , April , 85 8 , Peter J.

No comments compact multi-Fasta In this mode, the comments will be completely removed from the resulted multi-Fasta file. However the contents will be saved in a file, separated by a semicolon. This program is very small so you can easily copy it on a USB flash stick and take it with you or send it to your colleagues via email. Support Online Manual. Choose a name for the output file the default name is "Result 1" Press the 'Start' button.

Output format The program can generate three different types of multi-Fasta files: I. Portability This program is very small so you can easily copy it on a USB flash stick and take it with you or send it to your colleagues via email.