diff --git a/README.md b/README.md index bd07cfcfe19ecb51409f49f1f6ee2de6edd47b36..7c26698506c082ecd0520f40dd122ef1cbd033df 100644 --- a/README.md +++ b/README.md @@ -9,46 +9,23 @@ One of the older dogmata in molecular biology concerns proteins, and holds that > Sequence defines structure defines function. -In the past this was taken to mean that sequence similarity, above a certain threshold, correlated with sequence homology or even orthology. Sufficient sequence similarity was then inferred to mean high structural similarity (this was mostly proven by the success of homology modelling in CASP) as well as functional equivalence. In fact, "bidirectional best BLAST hits" is the _de facto_ default/baseline for functional annotation. +In the past this was taken to mean that sequence similarity, above a certain threshold, correlated with sequence homology or even orthology. Sufficient sequence similarity was then inferred to mean high structural similarity (this was mostly proven by the success of homology modelling in CASP) as well as functional equivalence. In fact, "bidirectional best BLAST hits" is the _de facto_ baseline for functional annotation. -The question of the threshold turns out to be an important one. Burkhardt Rost famously outlined it as the ["twilight zone"](https://pubmed.ncbi.nlm.nih.gov/10195279/) of protein similarity; briefly, while we can confidently assert structural similarity (at least to the fold level) for sequences with >30% sequence identity, this deteriorates impressively fast at 25% sequence identity. +The question of the threshold turns out to be an important one. Burkhardt Rost famously outlined it as the ["twilight zone"](https://pubmed.ncbi.nlm.nih.gov/10195279/) of protein similarity; briefly, while we can confidently assert structural similarity (at least to the fold level) for sequences with >30% sequence identity, this deteriorates impressively fast at 25% sequence identity. In the years since this pronouncement, sequence search algorithms with increased sensitivity exploited the mountains of new sequencing data to dive into the twilight zone and detect remote homology; however, at low sequence identity, the sequence information alone is still not enough to guarantee homology. -In the years since this pronouncement, sequence search algorithms with increased sensitivity exploited the mountains of new sequencing data to dive into the twilight zone and detect remote homology. - -A topic of particular interest for non-model organisms is that of functional annotation. - -The test case will be the proteome of the freshwater sponge _Spongilla lacustris_. - -## Badges -On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge. - -## Visuals -Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method. - -## Installation -Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection. +However, structure is more conserved than sequence. In theory, predicted structures can be compared against known structures that are otherwise annotated, allowing for the transfer of functional annotations (albeit less specific than sequence-based ones, since we will be detecting very remote homology at best). This is of particular interest for non-model organisms, especially ones outside the well-studied taxonomic groups (e.g. vertebrates or ecdysozoans). ## Usage -Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README. - -## Support -Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc. +(eventually a tutorial on what order to use the scripts in, if we don't have a master script). ## Roadmap -If you have ideas for releases in the future, it is a good idea to list them in the README. - -## Contributing -State if you are open to contributions and what your requirements are for accepting them. - -For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self. - -You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser. +We will write this in as general a way as possible so that it can be reused by others/for other species. Platynereis is an obvious candidate after we proof _Spongilla_. ## Authors and acknowledgment -Show your appreciation to those who have contributed to the project. +Fabian Ruperti, Niko Papadopoulos, Jacob Musser, Alexandros Pittis ## License -For open source projects, say how it is licensed. +MIT, probably? ## Project status -If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers. +ongoing