translate - determine the amino-acid sequence of a protein during its synthesis by using information on the messenger RNA rectify - math: determine the length of; "rectify a curve" redetermine - fix, find, or establish again; "the physicists redetermined Planck's constant" ...
Using the command line directly When PDBminer is run on only a single protein it may sometimes be beneficial to run it directly in the commandline. To do so, a input file does not need to be constructured and the content can be specified with flags. Again, the uniprot option is mandato...
4.1. Set the Parameter File The main configuration file for pIon is pIon.cfg. At a minimum, you need to set the paths to your FASTA file (protein sequence database) and your MS/MS data file(s). pIon supports the following MS/MS data formats: RAW, MZML, or MGF. Example configuration...
In the field of biological data mining, protein sequence classification is one of the most popular research area. To classify the protein sequence, features must be extracted from the input data. The...Suprativ SahaBrainware UniversityTanmay Bhattacharya...
By default the program makes queries based on all the protein residues in the input model, but a user defined fragment (e.g. most reliable) can be also specified with--selectkeyword. findmysequence --mtzin examples/1cbs_final.mtz --labin FWT,PHWT --modelin examples/1cbs_final.pdb -...
In response to this need, we propose a novel method called FindCSV, which leverages deep learning techniques and consensus sequences to enhance the detection of SVs using long-read sequencing data. Compared to current methods, FindCSV performs better in detecting complex and simple structural variat...
Fine-tuning these models on use case-specific datasets can improve accuracy. However, this requires large amounts of protein sequence, chemical structure, DNA/RNA sequence, assay data, images, text, and other data. This information is often spread across internal data lakes and extern...
For the completeness of this list, it is also necessary to site two major tools for the discovery and prediction of NPs from protein sequence data: antiSMASH [74] and PRISM [75]. Both are trained on, among others, NP data, but the latter is not provided directly to the public. ...
All the subsequent steps will be run. Note, most should not use this. Also this assumes things about type of sequencing reads. If using this script for analysis for publication, please talk to Nakul first.(1) Setup arguments.txtThe locations of the reference files need to be specified in ...
to increase both the generalization ability of predictive models and their robustness against changes in the structure of data (e.g., systematic drifts in the response variable) in diverse areas such as the analysis of spectroscopic data or the detection of conserved domains in protein sequences....