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Bioinformatics Tools and Software in Clinical Research
Published in Rishabha Malviya, Pramod Kumar Sharma, Sonali Sundram, Rajesh Kumar Dhanaraj, Balamurugan Balusamy, Bioinformatics Tools and Big Data Analytics for Patient Care, 2023
Deepika Bairagee, Nitu Singh, Neelam Jain, Urvashi Sharma
Sean Eddy created HMMER, a free and widely used software suite for sequence analysis. Its primary use is to find the required proteins with homologous nucleotide sequences and to perform series alignments. It discovers homology by comparing a profile-HMM with either a single sequence or a sequence database. Sequences that score significantly higher on the profile-HMM than a null design are considered homologous to the sequences utilized to create the profile-HMM [27]. The program build is used to create profile-HMMs from a multiple sequence alignment within the HMMER bundle. The HMMER program’s profile-HMM execution is based on Krogh and colleagues’ work. HMMER is a system tool that has been ported to Linux, Windows, and the macOS. Pfam and InterPro are two well-known protein databases that rely heavily on HMMER. Several additional BI tools, including UGENE [27,28], utilize HMMER.
Rapid communication: effects of cadmium exposure on the growth-related genes of Daphnia magna
Published in Journal of Toxicology and Environmental Health, Part A, 2022
Finally, a search was conducted on the transcribed genes for how many genes were related to growth. This was done by searching in water flea base (http://server7.wfleabase.org/genome/Daphnia_magna/openaccess/genes/Proteins/) for the sequence of primary and alternate isoform proteins of gene loci for Daphnia magna of the set of differentially expressed genes, which were identified in the database using the ID of genes provided by Orsini et al. (2016). With this information, homologous protein sequences were identified using HMMER 3.1b2 (2015) version 3.1b2 and protein family database Pfam repository (Mistry et al. 2020) release 32. All genes were classified with functional annotation of family proteins associated with exoskeleton formation as growth-related.