Results 11 to 20 of about 1,953,840 (266)

Designing hardware for protein sequence analysis [PDF]

Bioinformatics, 2003
Abstract We present the architecture of PROSIDIS, a special purpose co-processor designed to search for the occurrence of substrings similar to a given ‘template string’ within a proteome. Actual tests show speed up figures ranging from 5 to 50 with respect to conventional general-purpose processors.
Alessandro Marongiu, Paolo Palazzari, Vittorio Rosato   +2 more
openaire   +4 more sources

Progressive search in tandem mass spectrometry

BMC Bioinformatics, 2023
Background High-throughput Proteomics has been accelerated by (tandem) mass spectrometry. However, the slow speed of mass spectra analysis prevents the analysis results from being up-to-date.
Yoonsung Joh, Kangbae Lee, Hyunwoo Kim, Heejin Park   +3 more
doaj   +1 more source

SeqCP: A sequence-based algorithm for searching circularly permuted proteins

Computational and Structural Biotechnology Journal, 2023
Circular permutation (CP) is a protein sequence rearrangement in which the amino- and carboxyl-termini of a protein can be created in different positions along the imaginary circularized sequence.
Chi-Chun Chen, Yu-Wei Huang, Hsuan-Cheng Huang, Wei-Cheng Lo, Ping-Chiang Lyu   +4 more
doaj   +1 more source

iSeqSearch: incremental protein search for iBlast/iMMSeqs2/iDiamond [PDF]

PeerJ
Background The advancement of sequencing technology has led to a rapid increase in the amount of DNA and protein sequence data; consequently, the size of genomic and proteomic databases is constantly growing.
Hyunwoo Yoo, Mohammadsaleh Refahi, Robi Polikar, Bahrad A. Sokhansanj, James R. Brown, Gail L. Rosen   +5 more
doaj   +2 more sources

Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation

BMC Bioinformatics, 2021
Background The identification of protein families is of outstanding practical importance for in silico protein annotation and is at the basis of several bioinformatic resources.
Elena Tea Russo, Alessandro Laio, Marco Punta   +2 more
doaj   +1 more source

Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events

Frontiers in Bioinformatics, 2023
Protein annotation errors can have significant consequences in a wide range of fields, ranging from protein structure and function prediction to biomedical research, drug discovery, and biotechnology.
Arnaud Kress, Olivier Poch, Odile Lecompte, Julie D. Thompson   +3 more
doaj   +1 more source

Filtering Degenerate Patterns with Application to Protein Sequence Analysis

Algorithms, 2013
In biology, the notion of degenerate pattern plays a central role for describing various phenomena. For example, protein active site patterns, like those contained in the PROSITE database, e.g., [FY ]DPC[LIM][ASG]C[ASG], are, in general, represented by ...
Matteo Comin, Davide Verzotto
doaj   +1 more source

BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Biology Direct, 2022
Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes ...
Markus Sutter, Cheryl A. Kerfeld
doaj   +1 more source

Analysis of protein sequences [PDF]

Genome Biology, 2000
Several programs to predict sequence and structural features of a protein can be run simultaneously on the PredictProtein server.
openaire   +1 more source

Computational curation and analysis of publicly available protein sequence data from a single protein family

MethodsX, 2022
The wealth of sequence data available on public databases is increasing at an exponential rate, and while tremendous efforts are being made to make access to these resources easier, these data can be challenging for researchers to reuse because ...
Kyra Dougherty, Katalin A. Hudak
doaj   +1 more source