Japheth E. Gado

5 Questions 5 Answers 0 Followers

Questions related from Japheth E. Gado

How to search a profile HMM against a HMM database (HMM vs. HMMs)?

I have a set of n aligned protein sequences. I have constructed a profile hidden Markov model (HMM) from the alignment with hmmbuild in the HMMER package. I would like to compare my constructed...

23 September 2021 7,096 5 View

Fast way to compute pairwise identity matrix from multiple sequence alignment?

I have a multiple sequence alignment (MSA) of protein sequences in FASTA format. I will like to compute a sequence identity matrix that shows the sequence identity between each sequence and every...

15 June 2021 6,848 4 View

What is a fast way to retrieve protein sequences associated with a specific E.C. number?

Is there a quick way to retrieve proteins sequences associated with the E.C. number 3.1.1 from any of the protein databases (without database scraping)? How can I do this?

06 April 2021 6,282 4 View

How to identify motifs in a set of proteins that are not present in another set of proteins?

I have separated protein sequences of a particular family into two groups (according to some property). I will like to identify motifs that are present in the first group but absent from the...

24 July 2020 8,823 1 View

Is there any difference between Morgan fingerprints and ECFPs? What open-source tools are available for computing ECFPs?

I have a dataset of chemical structures and would like to compute ECFPs. I know that I can compute Morgan Fingerprints with RDKit, but these appear to be different from ECFPs...

10 July 2020 3,077 3 View