Global networks of functional coupling in eukaryotes from comprehensive data integration (2009)
Alexeyenko, Andrey, Sonnhammer, Erik L.L.
No single experimental method can discover all connections in the interactome. A computational approach can help by integrating data from multiple, often unrelated, proteomics and genomics pipelines....
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System (2009)
Messina, David N., Sonnhammer, Erik L. L.
Summary: The rise in biological sequence data has led to a proliferation of separate, specialized databases. While there is great value in having many independent annotations, it is critical that...
Comparative analysis and unification of domain-domain interaction networks (2009)
Björkholm, Patrik, Sonnhammer, Erik L. L.
Motivation: Certain protein domains are known to preferentially interact with other domains. Several approaches have been proposed to predict domain–domain interactions, and over nine datasets are...
Domain Tree-Based Analysis of Protein Architecture Evolution (2008)
Forslund, Kristoffer, Henricson, Anna, Hollich, Volker, Sonnhammer, Erik L. L.
Understanding the dynamics behind domain architecture evolution is of great importance to unravel the functions of proteins. Complex architectures have been created throughout evolution by...
InParanoid 6: eukaryotic ortholog clusters with inparalogs (2008)
Berglund, Ann-Charlotte, Sjölund, Erik, Östlund, Gabriel, Sonnhammer, Erik L. L.
The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available ‘complete’ eukaryotic proteomes...
The Pfam protein families database (2008)
Finn, Robert D., Tate, John, Mistry, Jaina, Coggill, Penny C., Sammut, Stephen John, Hotz, Hans-Rudolf, ...
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318...
jSquid: a Java applet for graphical on-line network exploration (2008)
Klammer, Martin, Roopra, Sanjit, Sonnhammer, Erik L. L.
Summary: jSquid is a graph visualization tool for exploring graphs from protein–protein interaction or functional coupling networks. The tool was designed for the FunCoup web site, but can be used...
Predicting protein function from domain content (2008)
Forslund, Kristoffer, Sonnhammer, Erik L. L.
Motivation: Computational assignment of protein function may be the single most vital application of bioinformatics in the post-genome era. These assignments are made based on various protein...
siRNA specificity searching incorporating mismatch tolerance data (2008)
Chalk, Alistair M., Sonnhammer, Erik L. L.
Artificially synthesized short interfering RNAs (siRNAs) are widely used in functional genomics to knock down specific target genes. One ongoing challenge is to guarantee that the siRNA does not...
Focusing on RISC assembly in mammalian cells (2008)
Hong, Junmei, Wei, Na, Chalk, Alistair Morgan, Wang, Jue, Song, Yutong, Yi, Fan, ...
RISC (RNA-induced silencing complex) is a central protein complex in RNAi, into which a siRNA strand is assembled to become effective in gene silencing. By using an in vitro RNAi reaction based on...
Focusing on RISC assembly in mammalian cells (2008)
Hong, Junmei, Wei, Na, Chalk, Alistair Morgan, Wang, Jue, Song, Yutong, Yi, Fan, ...
RISC (RNA-induced silencing complex) is a central protein complex in RNAi, into which a siRNA strand is assembled to become effective in gene silencing. By using an in vitro RNAi reaction based on...
siRNA specificity searching incorporating mismatch tolerance data (2008)
Chalk, Alistair Morgan, Sonnhammer, Erik L. L.
Artificially synthesized short interfering RNAs (siRNAs) are widely used in functional genomics to knock down specific target genes. One ongoing challenge is to guarantee that the siRNA does not...
siRNA specificity searching incorporating mismatch tolerance data (2008)
Chalk, Alistair Morgan, Sonnhammer, Erik L. L.
Artificially synthesized short interfering RNAs (siRNAs) are widely used in functional genomics to knock down specific target genes. One ongoing challenge is to guarantee that the siRNA does not...
Käll, Lukas, Krogh, Anders, Sonnhammer, Erik L.L.
When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods...
PfamAlyzer: domain-centric homology search (2007)
Hollich, Volker, Sonnhammer, Erik L.L.
Summary: PfamAlyzer is a Java applet that enables exploration of Pfam domain architectures using a user-friendly graphical interface. It can search the UniProt protein database for a domain pattern....
Abhiman, Saraswathi, Daub, Carsten O., Sonnhammer, Erik L. L.
Protein families typically embody a range of related functions and may thus be decomposed into subfamilies with, for example, distinct substrate specificities. Detection of functionally divergent...
Wistrand, Markus, Käll, Lukas, Sonnhammer, Erik L.L.
G protein-coupled receptors (GPCRs) constitute a large superfamily involved in various types of signal transduction pathways triggered by hormones, odorants, peptides, proteins, and other types of...
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment (2006)
Lassmann, Timo, Sonnhammer, Erik L. L.
Obtaining high quality multiple alignments is crucial for a range of sequence analysis tasks. A common strategy is to align the sequences several times, varying the program or parameters until the...
Wistrand, Markus, Käll, Lukas, Sonnhammer, Erik L.L.
G protein-coupled receptors (GPCRs) constitute a large superfamily involved in various types of signal transduction pathways triggered by hormones, odorants, peptides, proteins, and other types of...
Pfam: clans, web tools and services (2006)
Finn, Robert D., Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
Abhiman, Saraswathi, Daub, Carsten O., Sonnhammer, Erik L.L.
Protein families typically embody a range of related functions and may thus be decomposed into subfamilies with e.g. distinct substrate specificities. Detection of functionally divergent subfamilies...
Automatic clustering of orthologs and inparalogs shared by multiple proteomes (2006)
Alexeyenko, Andrey, Tamas, Ivica, Liu, Gang, Sonnhammer, Erik L.L.
Motivation: The complete sequencing of many genomes has made it possible to identify orthologous genes descending from a common ancestor. However, reconstruction of evolutionary history over long...
Wistrand, Markus, Käll, Lukas, Sonnhammer, Erik L.L.
G protein-coupled receptors (GPCRs) constitute a large superfamily involved in various types of signal transduction pathways triggered by hormones, odorants, peptides, proteins, and other types of...
siRNAdb: a database of siRNA sequences. (2005)
Chalk, Alistair Morgan, Warfvinge, Richard E., Georgii-Hemming, Patrik, Sonnhammer, Erik L. L.
Short interfering RNAs (siRNAs) are a popular method for gene-knockdown, acting by degrading the target mRNA. Before performing experiments it is invaluable to locate and evaluate previous knockdown...
siRNAdb: a database of siRNA sequences. (2005)
Chalk, Alistair Morgan, Warfvinge, Richard E., Georgii-Hemming, Patrik, Sonnhammer, Erik L. L.
Short interfering RNAs (siRNAs) are a popular method for gene-knockdown, acting by degrading the target mRNA. Before performing experiments it is invaluable to locate and evaluate previous knockdown...
siRNAdb: a database of siRNA sequences. (2005)
Chalk, Alistair Morgan, Warfvinge, Richard E., Georgii-Hemming, Patrik, Sonnhammer, Erik L. L.
Short interfering RNAs (siRNAs) are a popular method for gene-knockdown, acting by degrading the target mRNA. Before performing experiments it is invaluable to locate and evaluate previous knockdown...
siRNAdb: a database of siRNA sequences (2005)
Chalk, Alistair M., Warfinge, Richard E., Georgii-Hemming, Patrick, Sonnhammer, Erik L. L.
Short interfering RNAs (siRNAs) are a popular method for gene-knockdown, acting by degrading the target mRNA. Before performing experiments it is invaluable to locate and evaluate previous knockdown...
FunShift: a database of function shift analysis on protein subfamilies (2005)
Abhiman, Saraswathi, Sonnhammer, Erik L. L.
Members of a protein family normally have a general biochemical function in common, but frequently one or more subgroups have evolved a slightly different function, such as different substrate...
Inparanoid: a comprehensive database of eukaryotic orthologs (2005)
O'Brien, Kevin P., Remm, Maido, Sonnhammer, Erik L. L.
The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae,...
siRNAdb: a database of siRNA sequences (2005)
Chalk, Alistair M., Warfinge, Richard E., Georgii-Hemming, Patrick, Sonnhammer, Erik L. L.
Hollich, Volker, Milchert, Lena, Arvestad, Lars, Sonnhammer, Erik L.L.
Distance-based methods are popular for reconstructing evolutionary trees of protein sequences, mainly because of their speed and generality. A number of variants of the classical neighbor-joining...
Hollich, Volker, Milchert, Lena, Arvestad, Lars, Sonnhammer, Erik L. L.
Distance-based methods are popular for reconstructing evolutionary trees of protein sequences, mainly because of their speed and generality. A number of variants of the classical neighbor-joining...
Automatic assessment of alignment quality (2005)
Lassmann, Timo, Sonnhammer, Erik L. L.
Multiple sequence alignments play a central role in the annotation of novel genomes. Given the biological and computational complexity of this task, the automatic generation of high-quality...
An HMM posterior decoder for sequence feature prediction that includes homology information (2005)
Käll, Lukas, Krogh, Anders, Sonnhammer, Erik L. L.
Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil–coil structures, protein secondary structure or genes, extra support can be gained from homologs....
Hollich, Volker, Milchert, Lena, Arvestad, Lars, Sonnhammer, Erik L.L.
Distance-based methods are popular for reconstructing evolutionary trees of protein sequences, mainly because of their speed and generality. A number of variants of the classical neighbor-joining...
Improved and automated prediction of effective siRNA. (2004)
Chalk, Alistair Morgan, Wahlestedt, Claes, Sonnhammer, Erik L.L.
Short interfering RNAs are used in functional genomics studies to knockdown a single gene in a reversible manner. The results of siRNA experiments are highly dependent on the choice of siRNA...
Improved and automated prediction of effective siRNA. (2004)
Chalk, Alistair Morgan, Wahlestedt, Claes, Sonnhammer, Erik L.L.
Short interfering RNAs are used in functional genomics studies to knockdown a single gene in a reversible manner. The results of siRNA experiments are highly dependent on the choice of siRNA...
Sfixem—graphical sequence feature display in Java (2004)
Chalk, Alistair Morgan, Wennerberg, Martin, Sonnhammer, Erik L. L.
Sfixem is an sequence feature series (SFS) visualization tool implemented in Java. It is designed to visualize data from sequence analysis programs, allowing the user to view multiple sets of...
Sfixem—graphical sequence feature display in Java (2004)
Chalk, Alistair Morgan, Wennerberg, Martin, Sonnhammer, Erik L. L.
Sfixem is an sequence feature series (SFS) visualization tool implemented in Java. It is designed to visualize data from sequence analysis programs, allowing the user to view multiple sets of...
Improved and automated prediction of effective siRNA. (2004)
Chalk, Alistair Morgan, Wahlestedt, Claes, Sonnhammer, Erik L.L.
Short interfering RNAs are used in functional genomics studies to knockdown a single gene in a reversible manner. The results of siRNA experiments are highly dependent on the choice of siRNA...
Sfixem—graphical sequence feature display in Java (2004)
Chalk, Alistair Morgan, Wennerberg, Martin, Sonnhammer, Erik L. L.
Sfixem is an sequence feature series (SFS) visualization tool implemented in Java. It is designed to visualize data from sequence analysis programs, allowing the user to view multiple sets of...
ChromoWheel: a new spin on eukaryotic chromosome visualization (2004)
Ekdahl, Sven, Sonnhammer, Erik L. L.
Summary: ChromoWheel is an internet browser application for generating whole-genome illustrations. It can be used to depict chromosomes, genes, and relations between chromosomal loci. The circular...
Sfixem--graphical sequence feature display in Java (2004)
Chalk, Alistair M., Wennerberg, Martin, Sonnhammer, Erik L. L.
Summary: Sfixem is a SFS visualisation tool implemented in Java. It is designed to visualise data from sequence analysis programs, allowing the user to view multiple sets of computationally generated...
ChromoWheel: a new spin on eukaryotic chromosome visualization (2004)
Ekdahl, Sven, Sonnhammer, Erik L. L.
Summary: ChromoWheel is an Internet browser application for generating whole-genome illustrations. It can be used to depict chromosomes, genes and relations between chromosomal loci. The circular...
The Pfam protein families database (2004)
Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D., Hollich, Volker, Griffiths-Jones, Sam, ...
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for...
ChromoWheel: a new spin on eukaryotic chromosome visualization (2004)
Ekdahl, Sven, Sonnhammer, Erik L. L.
Summary: ChromoWheel is an internet browser application for generating whole-genome illustrations. It can be used to depict chromosomes, genes, and relations between chromosomal loci. The circular...
Sfixem--graphical sequence feature display in Java (2004)
Chalk, Alistair M., Wennerberg, Martin, Sonnhammer, Erik L. L.
Summary: Sfixem is a SFS visualisation tool implemented in Java. It is designed to visualise data from sequence analysis programs, allowing the user to view multiple sets of computationally generated...
Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database (2003)
Storm, Christian E.V., Sonnhammer, Erik L.L.
One of the most reliable methods for protein function annotation is to transfer experimentally known functions from orthologous proteins in other organisms. Most methods for identifying orthologs...
Genomic Gene Clustering Analysis of Pathways in Eukaryotes (2003)
Lee, Jennifer M., Sonnhammer, Erik L.L.
Genomic clustering of genes in a pathway is commonly found in prokaryotes due to transcriptional operons, but these are not present in most eukaryotes. Yet, there might be clustering to a lesser...
Computational Antisense Oligo Prediction with a Neural Network Model. (2002)
Chalk, Alistair Morgan, Sonnhammer, Erik L.L.
Motivation: The expression of a gene can be selectively inhibited by antisense oligonucleotides (AOs) targeting the mRNA. However, if the target site in the mRNA is picked randomly, typically 20% or...
Computational Antisense Oligo Prediction with a Neural Network Model. (2002)
Chalk, Alistair Morgan, Sonnhammer, Erik L.L.
Motivation: The expression of a gene can be selectively inhibited by antisense oligonucleotides (AOs) targeting the mRNA. However, if the target site in the mRNA is picked randomly, typically 20% or...
Computational Antisense Oligo Prediction with a Neural Network Model. (2002)
Chalk, Alistair Morgan, Sonnhammer, Erik L.L.
Motivation: The expression of a gene can be selectively inhibited by antisense oligonucleotides (AOs) targeting the mRNA. However, if the target site in the mRNA is picked randomly, typically 20% or...
The Pfam Protein Families Database (2002)
Bateman, Alex, Birney, Ewan, Cerruti, Lorenzo, Durbin, Richard, Etwiller, Laurence, Eddy, Sean R., ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at...
OrthoGUI: graphical presentation of Orthostrapper results (2002)
Hollich, Volker, Storm, Christian E. V., Sonnhammer, Erik L. L
Summary: Orthostrapper is a program that calculates orthology support values for pairs of sequences in a multiple alignment (Storm and Sonnhammer, Bioinformatics, 18, 92–99, 2002). Here we present...
Computational antisense oligo prediction with a neural network model (2002)
Chalk, Alistair M., Sonnhammer, Erik L. L.
Motivation: The expression of a gene can be selectively inhibited by antisense oligonucleotides (AOs) targeting the mRNA. However, if the target site in the mRNA is picked randomly, typically...
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability (2002)
Storm, Christian E. V., Sonnhammer, Erik L. L.
Motivation: Orthologous proteins in different species are likely to have similar biochemical function and biological role. When annotating a newly sequenced genome by sequencehomology, the most...
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs (2001)
Podowski, Raf M., Sonnhammer, Erik L. L.
Summary: MEDUSA is a tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects. The system allows specification of...
NIFAS: visual analysis of domain evolution in proteins (2001)
Storm, Christian E. V., Sonnhammer, Erik L. L.
Motivation: Multi-domain proteins have evolved by insertions or deletions of distinct protein domains. Tracing the history of a certain domain combination can be important for functional annotation...
The Pfam Protein Families Database (2000)
Bateman, Alex, Birney, Ewan, Durbin, Richard, Eddy, Sean R., Howe, Kevin L., Sonnhammer, Erik L. L.
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at...
A Workbench for large-scale sequence homology analysis (1994)
Sonnhammer, Erik L.L., Durbin, Richard
When routinely analysing very long stretches of DNA sequences produced by genome sequencing projects, detailed analysis of database search results becomes exceedingly time consuming. To reduce the...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Cerruti, Lorenzo, Durbin, Richard, Etwiller, Laurence, Eddy, Sean R., ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Durbin, Richard, Eddy, Sean R., Howe, Kevin L., Sonnhammer, Erik L. L.
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/ , in Sweden at...
The Pfam protein families database
Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D., Hollich, Volker, Griffiths-Jones, Sam, ...
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for...
Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database
Storm, Christian E.V., Sonnhammer, Erik L.L.
One of the most reliable methods for protein function annotation is to transfer experimentally known functions from orthologous proteins in other organisms. Most methods for identifying orthologs...
Genomic Gene Clustering Analysis of Pathways in Eukaryotes
Lee, Jennifer M., Sonnhammer, Erik L.L.
Genomic clustering of genes in a pathway is commonly found in prokaryotes due to transcriptional operons, but these are not present in most eukaryotes. Yet, there might be clustering to a lesser...
FunShift: a database of function shift analysis on protein subfamilies
Abhiman, Saraswathi, Sonnhammer, Erik L. L.
Members of a protein family normally have a general biochemical function in common, but frequently one or more subgroups have evolved a slightly different function, such as different substrate...
Inparanoid: a comprehensive database of eukaryotic orthologs
O'Brien, Kevin P., Remm, Maido, Sonnhammer, Erik L. L.
The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae,...
siRNAdb: a database of siRNA sequences
Chalk, Alistair M., Warfinge, Richard E., Georgii-Hemming, Patrick, Sonnhammer, Erik L. L.
Short interfering RNAs (siRNAs) are a popular method for gene-knockdown, acting by degrading the target mRNA. Before performing experiments it is invaluable to locate and evaluate previous knockdown...
siRNAdb: a database of siRNA sequences
Chalk, Alistair M., Warfinge, Richard E., Georgii-Hemming, Patrick, Sonnhammer, Erik L. L.
Automatic assessment of alignment quality
Lassmann, Timo, Sonnhammer, Erik L. L.
Multiple sequence alignments play a central role in the annotation of novel genomes. Given the biological and computational complexity of this task, the automatic generation of high-quality...
Pfam: clans, web tools and services
Finn, Robert D., Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment
Lassmann, Timo, Sonnhammer, Erik L. L.
Obtaining high quality multiple alignments is crucial for a range of sequence analysis tasks. A common strategy is to align the sequences several times, varying the program or parameters until the...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Cerruti, Lorenzo, Durbin, Richard, Etwiller, Laurence, Eddy, Sean R., ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Durbin, Richard, Eddy, Sean R., Howe, Kevin L., Sonnhammer, Erik L. L.
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/ , in Sweden at...
The Pfam protein families database
Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D., Hollich, Volker, Griffiths-Jones, Sam, ...
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for...
Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database
Storm, Christian E.V., Sonnhammer, Erik L.L.
One of the most reliable methods for protein function annotation is to transfer experimentally known functions from orthologous proteins in other organisms. Most methods for identifying orthologs...
Genomic Gene Clustering Analysis of Pathways in Eukaryotes
Lee, Jennifer M., Sonnhammer, Erik L.L.
Genomic clustering of genes in a pathway is commonly found in prokaryotes due to transcriptional operons, but these are not present in most eukaryotes. Yet, there might be clustering to a lesser...
FunShift: a database of function shift analysis on protein subfamilies
Abhiman, Saraswathi, Sonnhammer, Erik L. L.
Members of a protein family normally have a general biochemical function in common, but frequently one or more subgroups have evolved a slightly different function, such as different substrate...
Inparanoid: a comprehensive database of eukaryotic orthologs
O'Brien, Kevin P., Remm, Maido, Sonnhammer, Erik L. L.
The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae,...
siRNAdb: a database of siRNA sequences
Chalk, Alistair M., Warfinge, Richard E., Georgii-Hemming, Patrick, Sonnhammer, Erik L. L.
Short interfering RNAs (siRNAs) are a popular method for gene-knockdown, acting by degrading the target mRNA. Before performing experiments it is invaluable to locate and evaluate previous knockdown...
siRNAdb: a database of siRNA sequences
Chalk, Alistair M., Warfinge, Richard E., Georgii-Hemming, Patrick, Sonnhammer, Erik L. L.
Automatic assessment of alignment quality
Lassmann, Timo, Sonnhammer, Erik L. L.
Multiple sequence alignments play a central role in the annotation of novel genomes. Given the biological and computational complexity of this task, the automatic generation of high-quality...
Pfam: clans, web tools and services
Finn, Robert D., Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment
Lassmann, Timo, Sonnhammer, Erik L. L.
Obtaining high quality multiple alignments is crucial for a range of sequence analysis tasks. A common strategy is to align the sequences several times, varying the program or parameters until the...
Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server
Käll, Lukas, Krogh, Anders, Sonnhammer, Erik L.L.
When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods...
The Pfam protein families database
Finn, Robert D., Tate, John, Mistry, Jaina, Coggill, Penny C., Sammut, Stephen John, Hotz, Hans-Rudolf, ...
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318...
InParanoid 6: eukaryotic ortholog clusters with inparalogs
Berglund, Ann-Charlotte, Sjölund, Erik, Östlund, Gabriel, Sonnhammer, Erik L. L.
The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available ‘complete’ eukaryotic proteomes...
Wistrand, Markus, Käll, Lukas, Sonnhammer, Erik L.L.
G protein-coupled receptors (GPCRs) constitute a large superfamily involved in various types of signal transduction pathways triggered by hormones, odorants, peptides, proteins, and other types of...
Kemmer, Danielle, Faxén, Margareta, Hodges, Emily, Lim, Jonathan, Herzog, Elena, Ljungström, Elsebrit, ...
In this paper we aim to create a reference data collection of Northern blot results and demonstrate how such a collection can enable a quantitative comparison of modern expression profiling...
Lassmann, Timo, Frings, Oliver, Sonnhammer, Erik L. L.
In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data. To address this growing issue we have dramatically improved the running time and...