Metazoan SCP1 sequences used for protein alignment
Alignment of helical membrane protein sequences using AlignMe
... sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their ...
15
ComPotts: Optimal alignment of coevolutionary models for protein sequences
... Keywords Protein, sequence alignment, coevolution, Direct Coupling Analysis 1 Introduction Thanks to sequencing technologies, the number of available protein sequences has considerably ...
9
OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences
... of protein coding ...Commonly used alignment tools such as CLUSTAL and T- COFFEE [2,3] do not retain reading frame information, thus the achievement of in-frame alignments usually requires manual ...
6
OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences
... of protein coding ...Commonly used alignment tools such as CLUSTAL and T- COFFEE [2,3] do not retain reading frame information, thus the achievement of in-frame alignments usually requires manual ...
8
Unified Alignment of Protein-Protein Interaction Networks
... network alignment is the definition of a proper framework for combin- ing topology and sequence information to produce more biologically relevant network ...one used in Fuse, show promise in this ...schemes ...
11
Characterization, classification and alignment of protein-protein interfaces
... and used them for predicting interaction sites (Jones and Thornton, ...each protein surface was first split into ...in protein interaction sites by analyzing the distribution of hydrophobicity in ...
187
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
... final alignment and the library used by ...sidered alignment and its associated primary ...same sequences computed with different strategies for generating the primary ...the sequences ...
5
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
... final alignment and the library used by ...sidered alignment and its associated primary ...same sequences computed with different strategies for generating the primary ...the sequences ...
5
Intrinsic disorder in putative protein sequences
... nonsense sequences We created four datasets, one for each of the following species: Homo sapiens (human), Mus musculus (mouse), Drosophila melanogaster (fruitfly), Danio rerio (zebra- ...with sequences and ...
15
Prediction of Protein Function and Functional Sites From Protein Sequences
... full alignment of the whole Pfam database was ...4,687 sequences. The positive set consists of the sequences from 19 ...more sequences than others. To avoid bias, we only chose nine ...
149
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
... format used to define the genetic code for each species is the name of the taxon (or sequence) plus the index of the corresponding genetic code separated by a tab or comma ...multiple alignment programs ...
7
An Elitist Model for Obtaining Alignment of Multiple Sequences using Genetic Algorithm
... the alignment with each ...been used for searching large search space very efficiently but in increases time ...the sequences decreases complexity and shows some significant ...
7
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
... nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon ...sequence alignment method was ...
11
A New Algorithm for the Alignment of Phonetic Sequences
... After discussing various approaches to pho- netic alignment, I present a new algorithm that com- bines a number of techniques developed for se- quence comparison with a sco[r] ...
8
Efficient Alignment of Very Long Sequences
... We emphasize that the described cache model is a very simplified model. In practice, modern computers commonly have two or three levels of cache and em- ploy sophisticated adaptive cache replacement strategies rather ...
17
Comparison of DNA Sequences with Protein Sequences
... frameshift. Louis EST sequencing project (Hillier et al., 1996), the frequency of errors (substitutions, insertions, and deletions) in high-throughput EST sequencing ranges from about 2.5 to 7.5%. Mutations were cre- of ...
13
Protein-Protein Interaction Network Alignment
... network alignment. A significant amount of work has been done to reveal protein functions through analysis of PPI ...network alignment are the two main categories of network ...network ...
66
Clustering and Alignment of Polymorphic Sequences for HLA-DRB1 Genotyping
... are projected into diffusion space in which the Euclidean distance between two points is small if the points are highly connected in the original feature space and large otherwise. Then the K-means algorithm is applied ...
7
Improving performance of BWA alignment of short sequences with coroutines
... of sequences instead of just ...processing sequences in parallel, coordinated by cooperative scheduling as described in the previous ...the sequences evenly between each instance of Reg_Gap, the ...
ELIMINATE DUPLICATE URLs USING MULTIPLE ALIGNMENT OF SEQUENCES
... then used by a web crawler to avoid fetching DUST, including ones that are found for the first time during the ...criterion used to select these pairs and the availability of specific examples in the ...
6