Network Protein Sequence Analysis (NPSA, NPS@) image
This site is a fork of the original PRABI NPS@ server


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April 19th, 2024: NPS@ updated (see NEWS).


What's new in NPS@

April 2024
PROSITE database updated (20240327).
BCL-2 database (BCL2DB), Bacterial Tyrosine Kinase Database (BYKdb) and Hepatitis B Virus Database (HBVdb) updated.
Standard European Nucleotide Archive (20240210) updated.
Updated PSI-BLAST command line option (Smith-Waterman alignments) for consistency with BLAST.
Fixed missing residue display options in multiple sequence alignment result page.
Fixed "Empty sequence, no analysis can be performed !" message when performing "Consensus protein secondary structure prediction" from "Work with protein sequence" page (NPSA link).

March 2024
Updated Contact form to improve robustness against antispam filters.
Hardware and software upgraded. We apologize for disrupted service during first week of March.
Fixed protein secondary structure prediction consensus result page incorrectly displaying "No similar sequence found".

February 2024
PDB 3-D coordinates, PDB SEQRES, ESM Metagenomic Atlas (20230317) and Protein 3D sequences updated.
UniProt Knowledgebase updated (UniProtKB/Swiss-Prot+UniProtKB/TrEMBL 2024_01).
Put back PROSITE motifs / patterns / signatures scan (PROSCAN) for protein domains, families and functional sites annotation.

January 2024
Updated to set a minimum length of sequence for protein secondary structure prediction to 20 amino-acid residues to avoid long running computation (Consensus and MLRC).
PREDATOR protein secondary structure prediction method is now using a multiple sequence alignment as an input file.
Added missing links to PSI-BLAST an KALIGN multiple sequence alignment files in protein secondary structure prediction result page of MLRC, PREDATOR, SIMPA96 and Consensus.
Fixed SIMPA96 binary for incorrect input file reading with long sequence identifier. This change affects MLRC and Consensus predictions too.

December 2023
Added HMMER 3 profile HMM (Hidden Markov Models) HMMBUILD and HMMSEARCH tools for protein sequences (in replacement of deprecated HMMER 2).
Improved speed when extracting sequences from database after BLAST and FASTA package tool computations.
Fixed inconsistent alignments depending on KALIGN parameters by updating to version 3.4.0. This change affects DSC, SIMPA96, SOPMA, MLRC and Consensus predictions too.
Fixed SIMPA96 binary for incorrect format depending on multiple sequence alignment length and FASTA header length. These changes affect MLRC and Consensus predictions too.

November 2023
PDB 3-D coordinates, PDB SEQRES and Protein 3D sequences updated.
UniProt Knowledgebase updated (UniProtKB/Swiss-Prot+UniProtKB/TrEMBL 2023_05).
BLAST web form: added "BLOSUM90" option for "matrix" parameter.
PSI-BLAST web form:
- added "BLOSUM50", "BLOSUM90" and "PAM250" options for "matrix" parameter.
- decreased "Maximum number of passes to use in multipass version" from "2" to "1" to save CPU time and for query multi-domain protein.

October 2023
Fixed truncated displayed multiple sequence alignment (MSA) when their length > 8192 columns.
Fixed primary consensus string when there are >9 different residues with same frequency at a given multiple sequence alignment position (position now marked as '?' in the consensus).
Fixed DSC, MLRC and SIMPA96 protein secondary structure prediction binaries for long query sequences and large multiple sequence alignments. These changes affect Consensus prediction too.

August 2023
BCL-2 database (BCL2DB), Bacterial Tyrosine Kinase Database (BYKdb) and Hepatitis B Virus Database (HBVdb) updated.
Standard European Nucleotide Archive (20230616) updated.

July 2023
PDB 3-D coordinates, PDB SEQRES and Protein 3D sequences updated.
UniProt Knowledgebase updated (2023_03).
Sequence of length <7 residues are now discarded.
Fixed empty FASTA result with ktup=6 when searching viral genome sequence databases.
Fixed empty FASTA result when reverse nucleotide sequence pairwise alignments are reported.

June 2023
Fixed missing alignment data (length, identity, similar, different) in KALIGN, MAFFT and MUSCLE result page.
Fixed SIMPA96 binary for incorrect negative value in scale and updated to use multiple sequence alignment. These changes affect MLRC and Consensus predictions too.
Updated BLAST+ to version 2.14.0 with faster searches.
Updated FASTA/SSEARCH programs to version 36.3.8i, May 2023 with faster searches.
Updated FASTA/SSEARCH ktup parameter value range from 1 to 3 (default set to 3 from 2) for query protein sequence.
Fixed SOPMA prediction with huge multiple sequence alignment.

May 2023
BCL-2 database (BCL2DB), Bacterial Tyrosine Kinase Database (BYKdb) and Hepatitis B Virus Database (HBVdb) updated.
Fixed display of primary consensus of multiple nucleotide sequence alignment (was only displaying '-').

April 2023
This service was unavailable between April 19th and 30th following two power cuts in the city on April 19th and 23rd which affected a component of the network infrastructure. We apologize for the inconvenience caused.
Standard European Nucleotide Archive (20230310) updated.
UniProt Knowledgebase updated (2023_01) and divided into six sequence files: Fungi, Metazoa, Plants, Prokaryotes, Unclassified and Viruses.
PDB 3-D coordinates, PDB SEQRES and Protein 3D sequences updated.
Updated FASTA/SSEARCH ktup parameter value range from 3 to 6 (default set to 6 from 3) for query nucleotide sequence.
Opening of Geno3D fork site for comparative modelling of protein 3-D structure.
April 9th marks 25 years since NPS@ was made available. Many thanks to all NPS@'s users.

March 2023
Added KALIGN 3, MAFFT 7 and MUSCLE 5 multiple sequence alignment software.
Added BLAST+ version 2.13.0.
Added SSEARCH for query nucleotide sequence.
Added UniProtKB clustered sequence databases at 50, 70 and 90% identity for similarity search tools.
Added access to prediction result files in protein secondary structure prediction consensus.
Deleted CLUSTAL W and MULTALIN multiple sequence alignment software.
Deleted legacy BLAST version 2.2.26.
Updated BLAST/PSI-BLAST search parameters for short (<30 residues) query sequence.
Updated FASTA/SSEARCH programs to version 36.3.8i.
Updated FASTA/SSEARCH available parameters.
Updated multiple sequence alignment generation workflow for protein secondary structure prediction to fix long-running computations.
Updated SOPMA protein secondary structure prediction methods to use more sequences and to improve reproducibility.
Updated primary structure and 3-D structure analysis tools in NPSA link page.
Updated set of sequences to align size limit to 1,000,000 characters.
Updated upload file size limit to 20,000,000 characters.
Updated home page.
Fixed reading of FASTA/SSEARCH file when multiple alignment are displayed for a given subject sequence.
Fixed residue repertoire computation from the button available in multiple sequence alignment output page.

December 2022
BCL-2 database, Bacterial Tyrosine Kinase Database and Hepatitis B Virus Database updated.
Updated MSA generation for DSC and SOPMA protein secondary structure prediction methods (more sequences kept after filtering and use of MAFFT instead of Clustal W).

November 2022
UniProt Knowledgebase (2022_04) and Protein Data Bank updated.
AlphaFold2 Database (AlphaFoldDB, AF2DB), ESM Metagenomic Atlas and Protein Data Bank SEQRES added.
Protein 3D sequences added (AlphaFoldDB 50% identity + ESM Metagenomic Atlas High Confidence + PDB SEQRES 95% identity).
Non-Redundant Protein Sequences deleted.
Standard European Nucleotide Archive (20221006) updated and divided into six sequence files: Fungi (ENA-STD-FUN), Metazoa (ENA-STD-MET : HUM+INV+MAM+MUS+ROD+VRT), Others (ENA-STD-OTH : ENV+SYN+TGN+UNC+XXX), Plants (ENA-STD-PLN), Prokaryotes (ENA-STD-PRO) and Viruses (ENA-STD-VIR : PHG+VRL).
New two stages workflow for PSI-BLAST available.
Updated FASTA/SSEARCH programs to version 36.3.8h.
Protein secondary structure prediction methods available at this site.
Protein primary structure analysis methods available at this site.

August 2022
Standard European Nucleotide Archive (20220610), BCL-2 database, Bacterial Tyrosine Kinase Database and Hepatitis B Virus Database updated.

July 2022
Protein Data Bank and Non-Redundant Protein Sequences updated.

June 2022
UniProt Knowledgebase (2022_02) updated.

March 2022
Standard European Nucleotide Archive (20220202), BCL-2 database, Bacterial Tyrosine Kinase Database and Hepatitis B Virus Database updated.

February 2022
Protein Data Bank and Non-Redundant Protein Sequences updated.

January 2022
UniProt Knowledgebase (2021_04) updated.

June 2021
Protein Data Bank, Non-Redundant Protein Sequences, Standard European Nucleotide Archive (20210526), BCL-2 database, Bacterial Tyrosine Kinase Database and Hepatitis B Virus Database updated.

April 2021
UniProt Knowledgebase (2021_02) updated.

February 2021
Protein Data Bank, Non-Redundant Protein Sequences, Standard European Nucleotide Archive (20210120), BCL-2 database, Bacterial Tyrosine Kinase Database and Hepatitis B Virus Database updated.

December 2020
UniProt Knowledgebase (2020_06) updated.

October 2020
BCL-2 database, Bacterial Tyrosine Kinase Database and Hepatitis B Virus Database updated.

September 2020
Protein Data Bank, Non-Redundant Protein Sequences and Standard EMBL Nucleotide Sequence Database (renamed Standard European Nucleotide Archive, ENA; 20200909) updated.

August 2020
UniProt Knowledgebase (2020_04) updated.

July 2020
Standard EMBL Nucleotide Sequence Database (143.36), BCL-2 database, Bacterial Tyrosine Kinase Database and Hepatitis B Virus Database updated.

June 2020
UniProt Knowledgebase (2020_02), Protein Data Bank and Non-Redundant Protein Sequences updated.

February 2020
BCL-2 database, Bacterial Tyrosine Kinase Database and Hepatitis B Virus Database updated.

January 2020
Protein Data Bank, Non-Redundant Protein Sequences and Standard EMBL Nucleotide Sequence Database (142.27) updated.

December 2019
UniProt Knowledgebase (2019_10) updated.

December 2019
This fork of original PRABI NPS@ server opened.


Last modification time : Fri Apr 19 16:10:10 2024. Current time : Sat Apr 20 15:00:12 2024. User : public@35.174.62.162.

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