![]() ![]() So, it looks like I have a path to doing what I wanted in the first place - getting from. You can use GFF utilities to get a fasta sequence from a GFF file. Id just grab the bottom half of it, and if the sequence length looks right, thats likely what you want. But the file on your page has a fasta entry at the bottom. clustalw2 -tree -infile=droso.alnĪnd obtained a file droso.ph which looks like a Newick format file to me (some lines): ( It generally doesnt include sequence information, so you can not inter-convert. Sequence format conversion tools are available at. Line 7 parse the content of the sequence file and returns the content as the list. Then on Christoph's page, there is a section: If using sequences from NCBI we recommend saving them as FASTA format first. The extension, fasta refers to the file format of the sequence file. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists. ![]() Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. The RCSB PDB also provides a variety of tools and resources. This produces a droso.aln file which looks like this (only a few lines shown): D_paulistorum ETRVAEKLLEHPTQTTLACAQNFVKAIELNKNGAIWKLDLGTLEPIEWTKĭ_insularis ETRVAEKLLEHPTQTTLACAQNFVKAIELNKNGAIWKLDLGTLEPIEWTKĭ_equinoxialis ETRVAEKLLEHPTQTTLACAQNFVKAIELNKNGAIWKLDLGTLEPIEWTKĭ_willistoni ETRVAEKLLEHPTQTTLACAQNFVKAIELNKNGAIWKLDLGTLEPIEWTK As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. ![]() clustalw2 -align -type=protein -infile=droso.fasta Supports 200 + Formats of documents, images, presentations, archive, audio and video files. So, I had my clustalw2 executable and my 25 Drosophila alcohol dehydrogenase protein sequences and I ran the following commands (from Christoph's page). Powerful online file converter between multiple file formats. I tried compiling Clustalx (GUI - problem with qmake) which didn't work, but Clustalw (compiled to exe clustalw2) - the command line tool - worked a treat. Answer led me to and some searching led me to this page ( Christoph's). FASTA generator allows the user to convert seven MSA formats (ClustalW, MSF, Phylip, PIR, GDE, and Nexus) into FASTA format. ![]()
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