Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis (Q35914201)

11 August 2017

Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis (English)

1 reference

11 August 2017

1 reference

4

Kimmen Sjölander

0 references

author name string

Jake Gunn Glanville

1

1 reference

11 August 2017

Dan Kirshner

2

1 reference

11 August 2017

Nandini Krishnamurthy

3

1 reference

11 August 2017

Kimmen Sjölander

4

1 reference

11 August 2017

language of work or name

English

0 references

publication date

8 May 2007

1 reference

11 August 2017

Nucleic Acids Research

1 reference

11 August 2017

35

1 reference

11 August 2017

Web Server issue

1 reference

11 August 2017

W27-32

1 reference

FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Functional classification using phylogenomic inference

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

The Universal Protein Resource (UniProt)

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

A combined transmembrane topology and signal peptide prediction method

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

A comparison of scoring functions for protein sequence profile alignment.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Phylogenomic inference of protein molecular function: advances and challenges

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Domain shuffling has been the main mechanism forming new hominoid killer cell Ig-like receptors

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

The Pfam protein families database

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Signatures of domain shuffling in the human genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

ATV: display and manipulation of annotated phylogenetic trees

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Can sequence determine function?

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Gene ontology: tool for the unification of biology

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

11 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Predicting functions from protein sequences--where are the bottlenecks?

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Distinguishing Homologous from Analogous Proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Subfamily hmms in functional genomics.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

COACH: profile-profile alignment of protein families using hidden Markov models.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Phylogenetic inference in protein superfamilies: analysis of SH2 domains.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933202

Errors in genome annotation

24 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17488835

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17488835

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

SATCHMO: sequence alignment and tree construction using hidden Markov models

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17488835

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKM325

1 reference

journals/nar/GlanvilleKKS07

11 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

11 August 2017

1 reference