nebseq

Nebseq is a powerful Python module that allows for basic biological sequence manipulations. Those who are familiar with Python will find it quite easy to import, as it follows standard convention. One of the key features is the reverse complement function, which is extremely helpful when analyzing DNA or RNA. It should be noted, however, that revcomp does not check whether the inputted sequence is valid DNA or RNA. As long as the input sequence follows the expected format, the reverse complement will be accurately provided.

The translation function is also very useful, as it allows for full support of sequence translation. This includes the trimming of the first few bases, support for alternate translation tables, as well as support for the more esoteric post-translational modifications that can be found in some Genbank files. Also, partial peptides can be translated, allowing for fuzzy coordinates. By default, the first codon should be a start codon according to the selected translation table. If the first codon is not a start codon, then it will be converted to an "X".

The extract function is designed to allow users to slice out part of a larger sequence. This is particularly useful in conjunction with the nebgb module and its definition of locations parsed from strings such as join(1..5,9..100). This function is designed for convenience and ease of use.

Overall, the nebseq module is an outstanding tool for biological sequence manipulations. It is easy to use, reliable, and fast. The functions can be customized according to individual needs, allowing for great flexibility. Whether you're a beginner or someone who is more experienced in Python programming, you'll find the nebseq module to be a powerful tool in your workflow.