*Ancestral reconstruction

For example, PAML is a collection of programs for the phylogenetic analysis of DNA and protein sequence alignments by maximum ... These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the ... Since modern genetic sequences are essentially a variation of ancient ones, access to ancient sequences may identify other ... This allowed them to hypothesize a phylogeny for the sequences, and to infer that the standard sequence was probably also the ...

*Molecular phylogenetics

Bast, F. (2013). "Sequence Similarity Search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny ... The most common approach is the comparison of homologous sequences for genes using sequence alignment techniques to identify ... Modern sequence comparison techniques overcome this objection by the use of multiple sequences. Once the divergences between ... At any location within such a sequence, the bases found in a given position may vary between organisms. The particular sequence ...

*Structural alignment software

All Atoms Alignment; SSE -- Secondary Structure Elements Alignment; Seq -- Sequence-based alignment Pair -- Pairwise Alignment ... Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments". BMC Bioinformatics. 14 (24). doi: ... Brown, P.; Pullan W.; Yang Y.; Zhou Y. (Oct 2015). "Fast and accurate non-sequential protein structure alignment using a new ... This list of structural comparison and alignment software is a compilation of software tools and web portals used in pairwise ...

*Sequence alignment

Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple ... Sequence homology Sequence mining BLAST String searching algorithm Alignment-free sequence analysis UGENE Needleman-Wunsch ... alignments of two query sequences. Pairwise alignments can only be used between two sequences at a time, but they are efficient ... the short sequence should be globally aligned but only a local alignment is desired for the long sequence. Pairwise sequence ...

*Multiple sequence alignment

... tree alignment Phylogenetics Sequence alignment software Multiple sequence alignment viewers Structural alignment Alignment- ... A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or ... Multiple sequence alignment also refers to the process of aligning such a sequence set. Because three or more sequences of ... Multiple sequence alignment viewers enable alignments to be visually reviewed, often by inspecting the quality of alignment for ...

*List of sequence alignment software

This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment ... Sequence type: protein or nucleotide *Sequence type: protein or nucleotide **Alignment type: local or global *Sequence type: ... Alignment type: local or global *Sequence type: protein or nucleotide *Sequence type: protein or nucleotide Please see List of ... and multiple sequence alignment. See structural alignment software for structural alignment of proteins. * ...

*Alignment-free sequence analysis

... but when the sequences are divergent, a reliable alignment cannot be obtained and hence the applications of sequence alignment ... alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives over alignment-based ... pairwise or multiple sequence alignment. Alignment-based approaches generally give excellent results when the sequences under ... Sequence analysis Multiple sequence alignment Phylogenomics Bioinformatics Metagenomics Next-generation sequencing Population ...

*SH3D21

"Sequence Alignment". ALIGN. Retrieved 8 May 2013. ... Sequence identity was calculated using available sequence data ... In humans, these SH3 domains have a common amino acid sequence Asp-Glu-Leu. This sequence motif is also conserved in other ...

*Point accepted mutation

Point mutation Sequence alignment Margaret Dayhoff Molecular clock BLOSUM BLAST Campbell NA, Reece JB, Meyers N; Urry LA; Cain ... In bioinformatics, PAM matrices are regularly used as substitution matrices to score sequence alignments for proteins. Each ... Pevsner J (2009). "Pairwise Sequence Alignment". Bioinformatics and Functional Genomics (2nd ed.). Wiley-Blackwell. pp. 58-68. ... are also used as a scoring matrix when comparing DNA sequences or protein sequences to judge the quality of the alignment. This ...

*Inferring horizontal gene transfer

An Appraisal of Benchmarks for Multiple Sequence Alignment". Multiple Sequence Alignment Methods. Methods in molecular biology ... These tests assess the likelihood of the gene sequence alignment when the reference topology is given as the null hypothesis. ... Given simulated sequences which have HGT, analysis of those sequences using the methods of interest and comparison of their ... The donor sequences are inserted into the host unchanged or can be further evolved by simulation, e.g., using the tools ...

*C10orf76

"Sib Dotlet Sequence Alignment". Retrieved 13 May 2013. Pandey NB, Marzluff WF (Dec 1987). "The stem-loop structure at the 3' ... The following table illustrates the sequence similarity between human c10orf76 protein and various orthologs. Similar sequences ... "PredictProtein - Sequence Analysis, Structure and Function Prediction". Retrieved 18 April 2013. Lupas A, Van Dyke M, Stock J ( ... There are ten conserved potential phosphorylation sites within the protein sequence. Also, there are nine residues that are ...

*Clustal

Sequence alignment software DNASTAR Sequence mining T-Coffee Align-m DIALIGN-T DIALIGN-TX JAligner MAFFT MAVID MUSCLE ProbCons ... Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap ... All variants of Clustal align sequences by three main steps: Do a pairwise alignment Create a guide tree (or use a user-defined ... Multiple Sequence Alignment Methods. Methods in Molecular Biology. Humana Press. pp. 105-116. doi:10.1007/978-1-62703-646-7_6. ...

*BAli-Phy

Output alignments include homology information for sequences at internal nodes of the tree. Sequence alignment software ... BAli-Phy is a free software program for simultaneously estimating a multiple sequence alignment and its phylogenetic tree. BAli ... BAli-Phy takes alignment uncertainty into account while estimating the phylogeny by averaging over possible alignments. Unlike ... Alignment uncertainty stems from two main sources: near-optimal alignments and evolutionary parameter uncertainty. Evolutionary ...

*PANDIT (database)

Phylogeny Sequence alignment Whelan, Simon; de Bakker Paul I W; Quevillon Emmanuel; Rodriguez Nicolas; Goldman Nick (Jan 2006 ... PANDIT is a database of multiple sequence alignments and phylogenetic trees covering many common protein domains. ...

*TMEM229B

See multiple sequence alignment below. Annotated diagram of the TMEM229b gene (with its 3 exons), mature mRNA and protein ... Expressed Sequence Tag mapping of TMEM229B gene expression indicates that it is ubiquitously expressed throughout the body. ... "NCBI Nuceleotide BLAST". Basic Local Alignment Search. "EST profile: TMEM229B". UniGene. National Library of Medicine. ...

*MUSCLE (alignment software)

Sequence alignment software DNASTAR Clustal ProbCons AMAP T-COFFEE MAFFT Edgar RC (2004). "MUSCLE: multiple sequence alignment ... MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and ... "MUSCLE < Multiple Sequence Alignment < EMBL-EBI". Retrieved 1 September 2014. "Robert C. Edgar - Google Scholar Citations". ... The first paper, published in Nucleic Acids Research, introduced the sequence alignment algorithm. The second paper, published ...

*DECIPHER (software)

Sequence databases: import, maintain, view, and export sequences. Multiple sequence alignment: align sequences of DNA, RNA, or ... Sequence alignment software Wright ES (2015). "DECIPHER: harnessing local sequence context to improve protein multiple sequence ... Genome alignment: find and align the syntenic regions of multiple genomes. Oligonucleotide design: primer design for polymerase ... Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with ...

*Ewan Birney

... publications indexed by Google Scholar Birney, Ewan (2000). Sequence alignment in bioinformatics (PhD thesis). ... Feb 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. Bibcode:2001Natur.409..860L. doi ... He has played a role in annotating the genome sequences of the human, mouse, chicken and several other organisms. His research ... He wrote the first error tolerant, splice aware protein alignment program, used in the human and subsequent genome analysis; he ...

*MAFFT

In bioinformatics, MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. The software is named ... Sequence alignment software Clustal Katoh, Kazutaka; Misawa, Kazuharu; Kuma, Kei-ichi; Miyata, Takashi (2002). "MAFFT: a novel ... improvement in accuracy of multiple sequence alignment". Nucleic Acids Research. 33 (2): 511-8. doi:10.1093/nar/gki198. PMC ... method for rapid multiple sequence alignment based on fast Fourier transform". Nucleic Acids Research. 30 (14): 3059-66. doi: ...

*Align-m

... multiple sequence alignment, include extra information to guide the sequence alignment, multiple structural alignment, homology ... combining many alignments into one consensus sequence, multiple genome alignment (can cope with rearrangements). Sequence ... combining sequence and structure alignment data, 'filtering' of BLAST or other pairwise alignments, ... Align-m is a multiple sequence alignment program written by Ivo Van Walle. Align-m has the ability to accomplish the following ...

*Richard M. Durbin

Birney, Ewan (2000). Sequence alignment in bioinformatics (PhD thesis). University of Cambridge. Holmes, Ian (1999). Studies in ... c. Elegans Sequencing, C. (1998). "Genome sequence of the nematode C. Elegans: A platform for investigating biology". Science. ... More recently Durbin has returned to sequencing and has developed low coverage approaches to population genome sequencing, ... February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. doi:10.1038/35057062. ISSN ...

*2D gel analysis software

Sequence alignment software Biological data visualization. ...

*Lorraine Lisiecki

... for probabilistic sequence alignment of stratigraphic records. Paleoceanography software designed to find the optimal alignment ... "Probabilistic sequence alignment of stratigraphic records". Paleoceanography. 29. doi:10.1002/2014pa002713. "Match Software". ... In the LR04, there are higher resolution records, an improved alignment technique, and a higher percentage of records from the ... Lisiecki's Ph.D. thesis was titled "Paleoclimate time series: New alignment and compositing techniques, a 5.3-Myr benthic δ18O ...

*Circular permutation in proteins

Sequence-based algorithms require only the sequence of two proteins in order to create an alignment. Sequence methods are ... Traditional algorithms for sequence alignment and structure alignment are not able to detect circular permutations between ... Many sequence alignment and protein structure alignment algorithms have been developed assuming linear data representations and ... Zuker, M. (1991). "Suboptimal sequence alignment in molecular biology. Alignment with error analysis". Journal of Molecular ...

*Bacterial phylodynamics

Multiple sequence alignment algorithms can leave a large amount of indels in the sequence alignment when the indels do not ... Multiple sequence alignment algorithms (e.g., MUSCLE, MAFFT, and CLUSAL W) will align the data set with all selected sequences ... After the running a multiple sequence alignment algorithm, manual editing the alignment is highly recommended. ... If phylogenetic signal of an alignment is too low then a longer alignment or an alignment of another gene in the organism may ...

*Baum-Welch algorithm

Bishop, Martin J.; Thompson, Elizabeth A. (20 July 1986). "Maximum likelihood alignment of DNA sequences". Journal of Molecular ... This is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 ... The GENSCAN webserver is a gene locator capable of analyzing eukaryotic sequences up to one million base-pairs (1 Mbp) long. ... The feature is then compared to all sequences of the speech recognition units. These units could be phonemes, syllables, or ...

*LRRN3

A multiple sequence alignment has shown this very high conservation of the LRRN3 gene among many different species. All 12 of ... Multiple Sequence Alignment". [permanent dead link] "UniGene: Leucine-Rich Repeat Neuronal 3". "Allen Brain Atlas: Leucine-Rich ... The Ig and FN3 domains also show high conservation in all of the orthologous sequences for mammals and birds, but are not as ... The LINGO1 ectodomain also has a very long stretch of leucine-rich repeats which is the region that has the best alignment with ...