Due to NGLView (the Python module) having a frozen older IPywidget version it breaks Colab and the major change for the latter library was a year ago (early 2023), so I am forced to revisit old code and switch to py3Dmol in my Colab demos. Today I figured out how to use custom carbon colours.
Showing posts with label javascript. Show all posts
Showing posts with label javascript. Show all posts
Monday, 22 January 2024
Tuesday, 6 October 2015
PrettyFastaJS
I wrote a small script to allow one to easily and prettily embed both nucleic acid and protein FASTA sequences on a webpage (it guesses based on EFILPQ which are not degerate bases, but residues). It was a mix of "I need this" and "I want to play with colours". The latter was rather painful. But the result is a JS modified and CSS coloured fasta files.
The files can be found in my GitHub repository for PrettyFastaJS and so are the explanations of how to use it. As a demo, here are two curious sequences. Two consecutive genes in the same operon that encode each a full length glycine dehydrogenases, which in other species is a homodimer, which suggests this may be a cool heterodimer.
The files can be found in my GitHub repository for PrettyFastaJS and so are the explanations of how to use it. As a demo, here are two curious sequences. Two consecutive genes in the same operon that encode each a full length glycine dehydrogenases, which in other species is a homodimer, which suggests this may be a cool heterodimer.
>Gthg02641 Glycine dehydrogenase (EC 1.4.4.2) [Geobacillus thermoglucosidasius TM242]
MLKNWGIAMHKDQPLIFELSKPGRIGYSLPELDVPAVRVEEVVPADYIRTEEPELPEVSELDIMRHYTALSKRNHGVDSGFYPLGSCTMKYNPKINENVARLAGFAHIHPLQPEETVQGALELMYDLQEHLKEITGMDAVTLQPAAGAHGEWTGLMMIRAYHEANGDFQRTKVIVPDSAHGTNPASATVAGFETITVKSTEDGLVDLEDLKRVVGPDTAALMLTNPNTLGLFEENILEMAKIVHDAGGKLYYDGANLNAVLSKARPGDMGFDVVHLNLHKTFTGPHGGGGPGSGPVGVKADLIPFLPKPVVEKGENGYYLDDDRPQSIGRVKPFYGNFAINVRAYTYIRSMGPEGLKAVAEYAVLNANYMMRRLAEYYDLPYDRHCKHEFVLSGKRQKKLGVRTLDIAKRLLDFGFHPPTVYFPLIVEECMMIEPTETESKETLDAFIDAMIQIAKEAEENPEIVQEAPHTTVVKRLDETKAARKPILRYQKQ
>Gthg02642 Glycine dehydrogenase (EC 1.4.4.2) [Geobacillus thermoglucosidasius TM242]
MLHRYLPMTEEDKREMLNVIGVDSIDDLFADIPESVRFRGELNIKKAKSEVELWKELSALAAKNADVKKYTSFLGAGVYDHYIPAIVDHVISRSEFYTAYTPYQPEISQGELQAIFEFQTMICELTGMDVANSSMYDGGTALAEAMLLSAAHTKKKKVLLAKTVHPEYRGVVKTYAKGQRLHVVEIPFQHGVTDLEALKAEMDDEVACVIVQYPNFFGQIEPLKDIEPVAHSCKSMFVVASNPLALGILAPPGKFGADIVVGDVQPFGIPMQFGGPHCGYFAVKAELMRKIPGRLVGQTTDEEGRRGFVLTLQAREQHIRRDKATSNICSNQALNALAASVAMTALGKKGIKEMATMNIQKAQYAKNELVKHGFAVPFTGPFFNEFVVCLAKPVAEVNKQLLRKGIIGGYDVGRDYPELQNHMLIAVTELRTKEEIDMFVKELGDCHA
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