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Articles tagged: Fasta

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Posted by Ville Koskinen (August 31, 2022)

Downloading UniProt proteomes via new API

The UniProt website received a snazzy facelift in June 2022. Both the browser interface and the REST API were updated. The previous version, now termed legacy website, remains available until the 2022_04 release under a new URL (https://legacy.uniprot.org/) – so there is limited time to compare and admire the improvements! The new API is an almost seamless transition for Mascot [...]

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Posted by Ville Koskinen (April 19, 2022)

NCBI nr in Mascot Server 2.8.1

Mascot Server 2.8.01 patch was released in March 2022. One of the big improvements is optimising the compression speed of the NCBI nr database, available as the NCBIprot predefined definition. We’ve greatly decreased the time it takes to bring the database online, as well as removed an inadvertent limitation on database size. The patch is available to download on the [...]

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Posted by Richard Jacob (September 16, 2020)

The minutiae of database management

The two major inputs into a database search are sequence databases and mass spectrometry data. Management of the databases in Mascot Server has evolved and improved over the years and newer versions. There are still a few issues that come up regularly and I am going to cover them in this article. Common error messages When you activate a new [...]

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Posted by John Cottrell (December 17, 2019)

Protein FDR in Mascot Server 2.7

One of the new features in Mascot Server 2.7, now running on this web site, is an estimate of protein FDR. This is displayed in the Protein Family Summary for Fasta searches whenever automatic decoy is selected. The basis is the number of proteins inferred in the target database compared with the number in the decoy database. Conceptually, this is [...]

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Posted by John Cottrell (June 14, 2019)

What are you inferring?

Benchmarking protein inference is notoriously difficult. Artificial samples of known content tend to be too simple while real samples lack ground truth. An interesting approach was adopted for the ABRF iPRG 2016 study, and has been the subject of a publication from The et al. A collection of human Protein Epitope Signature Tags (PrESTs) were expressed in E. coli and [...]

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Posted by Ville Koskinen (April 13, 2018)

Keeping genome databases up to date

Database Manager is a great tool for keeping your sequence databases up to date in Mascot. If the database is available as a ready-made FASTA file, all you need to do is enable it as a predefined definition, or set up a definition to download the file from a known URL (see the help for more details). Updating the database [...]

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Posted by John Cottrell (September 12, 2017)

How to create a spectral library for contaminants

An earlier article highlighted how modified and non-specific peptides from contaminants can be matched using a spectral library without increasing the search space for the target proteins. This is particularly useful for sequencing grade trypsin, which is modified by methylation or acetylation of the lysines, creating a large number of modified non-specific peptides that are missed by typical search strategies. [...]

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Posted by John Cottrell (January 14, 2016)

Disruption ahead for NCBI databases

NCBI has announced that it will drop ‘gi number’ unique identifiers on June 15, 2016. Details are given in section 1.4 of the GenBank release notes. This will create difficulties for users of many bioinformatic tools, not just Mascot. Particularly in the context of major projects, where analyses are performed over an extended time period and results consolidated by protein [...]

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