Results 71 to 80 of about 1,296,938 (317)
BMC Bioinformatics, 2011 Background Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif ...
Deng Xin, Cheng Jianlin
doaj +1 more source
FEBS Letters, EarlyView.We present the first solution structure of the Ca2+‐depleted LETM1 F‐EF‐hand through a D676A/N678A Ca2+ binding‐deficient mutant, revealing a closed hydrophobic cleft caused by a unique F1‐helix pivot. The apo LETM1 F‐EF‐hand exhibits regiospecific hot and cold unfolding, sensitivity to physiological pH changes and potential for promiscuous heterotypic
Qi‐Tong Lin +2 more
wiley +1 more source
Iterative refinement of structure-based sequence alignments by Seed Extension
BMC Bioinformatics, 2009 Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone.
Lee Byungkook +2 more
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Insertion of the FeB cofactor in cNORs lacking metal inserting chaperones
FEBS Letters, EarlyView.Nitric oxide reductase is an enzyme found in the bacterial denitrification pathway. The NOR active site contains a non‐heme iron, often, but not always inserted with the assistance of chaperones. Here, we study the insertion of FeB in the subfamily of cNORs lacking chaperones and found a putative channel, conserved in the family, perhaps enabling the ...
Sofia Appelgren, Pia Ädelroth
wiley +1 more source
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM [PDF]
arXiv, 2013 Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment.
arxiv
FEBS Letters, EarlyView.LHCPs are transported to the thylakoid membrane via the (cp)SRP pathway. This process involves a transit complex of (cp)SRP43, (cp)SRP54 and LHCP, which interacts with (cp)FtsY and Alb3 at the membrane. GTP hydrolysis by (cp)SRP54 and (cp)FtsY triggers complex dissociation.
Victor Zegarra +7 more
wiley +1 more source
Pangenomic genotyping with the marker array
Algorithms for Molecular Biology, 2023 We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array.
Taher Mun +2 more
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HQAlign: Aligning nanopore reads for SV detection using current-level modeling [PDF]
arXiv, 2023 Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate alignment of these long reads play an important role in identifying novel SVs.
arxiv
FEBS Letters, EarlyView.This study explores the distinct molecular mechanisms underlying Lynch syndrome‐associated and sporadic colorectal cancer (CRC). By highlighting the therapeutic potential of targeting the PI3K‐Akt pathway in Lynch syndrome‐associated CRC and the Wnt pathway in sporadic CRC, the findings open avenues for personalised treatment strategies, aiming to ...
May J. Krause +2 more
wiley +1 more source
Local alignment of two-base encoded DNA sequence
BMC Bioinformatics, 2009 Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base ...
Merriman Barry +2 more
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