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Articles by Tim Ashby
Public Safety Center Replace Chilled Water Coils in AHU-4B & 4C (RFB No. 26-021).
ADVERTISEMENT FOR BIDS Sealed proposals will be received by County of Wake in the Procurement Services, in Suite 2900, Wake County Justice Center, 301 S. McDowell Street, Raleigh, NC 27601, for providing labor, material, and equipment entering into Single Prime Mechanical Prime Contract for the Public Safety Center Replace Chilled Water Coils in AHU-4B & 4C (RFB No. 26-021).
Smith-Waterman Algorithm for Local Alignment
Pairwise sequence alignment is a fundamental technique in bioinformatics that involves comparing two sequences of DNA, RNA, or proteins to identify and quantify similarity. These similarities can indicate functional, structural, or evolutionary relationships between the sequences. The process can be performed using global alignment, which aligns the entire length of both sequences, or local alignment, which focuses on aligning the most similar subsequences within the larger sequences.
Affine Gap Penalties for Scoring Pairwise Alignments
A scoring function for pairwise sequence alignment is crucial for two major reasons. First, the scoring function provides a quantitative measure of how two sequences align. This allows for an objective comparison between different alignments and the determination of the optimal alignment. Second, by assigning scores to matches, mismatches, and gaps (insertions or deletions), the scoring function can reflect the biological significance of sequence similarity and dissimilarity.
Coding Needleman-Wunsch for Global Sequence Alignment in Python
By Tim Ashby Photo by Edz Norton on Unsplash In our last post in this series, we discussed how Needleman-Wunsch works at a fundamental level. To remind you, Needleman-Wunsch is an algorithm that permits us to find the optimal global alignment for two biological sequences given a scoring function. We are going to take this a step farther and consider how to do this in Python. We will also cover how...
Comparing Biological Sequences in Python
Comparing Biological Sequences in Python Photo by Melanie Dijkstra on Unsplash A fundamental task of bioinformatics is being able to compare two sequences, whether or not those sequences happen to be DNA, RNA, or protein. We compare sequences to understand their relationship. There are several reasons why we might do this. First, it would simply be error checking: How does the sequence I have saved on my computer agree (or disagree) with the canonical sequence from NCBI? Second, we can compare…
Computing GC Content of a Nucleic Acid Sequence with Python
Nucleic acids include DNA and RNA. DNA has four nucleotide bases: adenine (A), cytosine (C), guanine (G), and thymine (T). RNA also has four: A, C, and G are the same, but T is replaced by uracil (U). Moving back and forth between DNA and RNA sequences is no big deal. Neither is counting the number of each base in our sequence.
Translating Nucleic Acid Sequences to Amino Acid Sequences with Python
The central dogma of molecular biology stipulates that our genetic material (DNA) is first transcribed into a temporary form (messenger RNA) before being translated into its protein sequence. The act of translation is akin to translation as we use it when talking about languages, i.e., translating English to French. We are taking an alphabet of nucleic acids (A, T, C, and G) and rewriting this in the language of amino acids (and there are 20 amino acids).
DNA Transcription and Reverse Complements with Python
The central dogma of molecular biology stipulates that information stored in the biological source code (DNA) is copied to a temporary form (messenger RNA) that is then used to create a functional product (proteins). Although the central dogma has been questioned and expanded upon since its postulation during the turn of the century, it still provides the pathway by which many proteins are created.
Counting Nucleotides in DNA Sequences with Python
One of the most fundamental tasks of bioinformatics is counting nucleotides in DNA sequences. Why is counting nucleotides important? Nucleotide counts can be used to validate and verify that the sequence we have on hand is the sequence we expect to have. Data can get corrupted or overwritten over time, so keeping track of our nucleotide counts is one way to ensure file integrity. Nucleotide counts can be use to investigate organismal differences.
Public Safety Center Dorms VAV Box Replacement (RFB No. 22-086)
by GDN Job Post November 15, 2022 RE-ADVERTISEMENT FOR BIDS Sealed proposals will be received by County of Wake in the Procurement Services, Wake County Justice Center, 301 S. McDowell Street, Suite 2900, Raleigh, NC 27601 for providing labor, material and equipment entering into Single Mechanical Prime Contract for the Public Safety Center Dorms VAV Box Replacement (RFB No. 22-086). Sealed Single Prime bids will be received until 2:00 p.m. on December 6, 2022.
Public Safety Center Dorms VAV Box Replacement (RFB No. 22-086).
by GDN Job Post October 5, 2022 ADVERTISEMENT FOR BIDS Sealed proposals will be received by County of Wake in the Procurement Services, Wake County Justice Center, 301 S. McDowell Street, Suite 2900, Raleigh, NC 27601 for providing labor, material and equipment entering into Single Mechanical Prime Contract for the Public Safety Center Dorms VAV Box Replacement (RFB No. 22-086). Sealed Single Prime bids will be received until 2:00 p.m. on November 8, 2022.
HVAC System Replacement at the Firearms Training Center (RFB No. 21-087)
by GDN Job Post October 5, 2021 ADVERTISEMENT FOR BIDS Sealed proposals will be received by County of Wake in the Procurement Services, Wake County Justice Center, 301 S. McDowell Street, Suite 2900, Raleigh, NC 27601 for providing labor, material and equipment entering into Single Mechanical Prime Contract for the HVAC System Replacement at the Firearms Training Center (RFB No. 21-087). Sealed Single Prime bids will be received until 2:00 p.m. on November 9, 2021.
Marbles Kids Museum/IMAX Theater Chillers Replacement (RFB No. 21-068)
by GDN Job Post September 2, 2021 ADVERTISEMENT FOR BIDS Sealed proposals will be received by County of Wake in the Procurement Services, Wake County Justice Center, 301 S. McDowell Street, Suite 2900, Raleigh, NC 27601 for providing labor, material and equipment entering into Single Mechanical Prime Contract for the Marbles Kids Museum/IMAX Theater Chillers Replacement (RFB No. 21-068). Sealed Single Prime bids will be received until 2:00 p.m. on September 28, 2021.
Fund my Dreams!!
My name is Tim Ashby, and in case you somehow don't know, I'm an actor. I am so passionate about the art/craft and have been for almost 10 years, and I have some greaaattt opportunities coming up. I was one of 10 actors accepted into Ohio University's MFA Acting program from the fall of 2015 to the spring of 2018. I also recently got accepted to participate in a 4 day workshop with the legendary acting coach, Larry Moss.
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