Pratt statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Pratt
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Tool usage distribution map

This map represents all the scientific publications referring to Pratt per scientific context
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Protocols

Pratt specifications

Information


Unique identifier OMICS_19711
Name Pratt
Interface Web user interface
Restrictions to use None
Input data A set of protein sequences.
Input format FASTA, UnioProtKB, SwissProt
Computer skills Basic
Stability Stable
Maintained Yes

Additional information


http://www.ebi.ac.uk/Tools/pfa/pratt/help/

Pratt citations

 (7)
library_books

Identification of ATP Binding Regions in the RyR1 Ca2+ Release Channel

2012
PLoS One
PMCID: 3492408
PMID: 23144945
DOI: 10.1371/journal.pone.0048725

[…] leotide binding sites using the reported consensus nucleotide binding motifs: GXGXXG, [R/K]XXXGXXXL and Y[G/A/S/T][V/G][K/T/Q/S/N] , with ScanProsite (http://prosite.expasy.org/scanprosite/) and EBI PRATT server (http://www.ebi.ac.uk/Tools/pratt/). Secondary structure prediction was performed using the PSIPRED Protein Structure Prediction Server (http://bioinf.cs.ucl.ac.uk/psipred/). Multiple seq […]

call_split

Phylogenetic study of nine species of freshwater monogeneans using secondary structure and motif prediction from India

2012
Bioinformation
PMCID: 3489091
PMID: 23144541
DOI: 10.6026/97320630008862
call_split See protocol

[…] 28S sequence motifs were identified from the aligned sequences by using PRATT software (http://www.ebi.ac.uk/pratt/). The C% parameter was adjusted to report pattern matching at 100% of the sequences input. The motifs were expressed by using the DNA alphabet (A, T, C, G) […]

library_books

Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties

2008
BMC Evol Biol
PMCID: 2533329
PMID: 18673550
DOI: 10.1186/1471-2148-8-225

[…] fined in each TRIM and TRIM-like protein by hand using the previously published patterns []. In order to obtain a new profiling, the sequences corresponding to each domain were then aligned using the PRATT 2.1 program [] and the best scoring consensi were selected and integrated by hand. The order of the sequences in the alignment shown reflects their degree of sequence conservation. The region of […]

call_split

Unique motifs identify PIG A proteins from glycosyltransferases of the GT4 family

2008
BMC Evol Biol
PMCID: 2446393
PMID: 18522757
DOI: 10.1186/1471-2148-8-168
call_split See protocol

[…] Rooted tree was built using TreeTop program, available from GeneBee Molecular Biology server [], and unrooted tree was built using Phylodendron [].Motifs were identified manually as well as by using PRATT [] and Gblocks software [,,]. The motifs identified manually were represented in the Prosite format and were used to search the Swiss-Prot and TrEMBL databases with match mode of greedy, overlap […]

library_books

LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana

2008
BMC Genomics
PMCID: 2292704
PMID: 18318901
DOI: 10.1186/1471-2164-9-118

[…] their sequence homology to the stored Pfam domains []. In the Prosite [,] database, two patterns defining dehydrins are present. For most of the other groups, we were able to create patterns with the PRATT [,] tool. The PATTINPROT [,] tool was used to verify the stringency of the retrieved patterns by querying the UniProt [,] database. To get more information about the nature of the gene products, […]

library_books

Evaluating deterministic motif significance measures in protein databases

2007
PMCID: 2254621
PMID: 18157916
DOI: 10.1186/1748-7188-2-16

[…] For flexible gap motifs, a slightly different experiment was performed. In this case, it was evaluated how Information-theoretic measures relate to the Pratt measure.The Pratt algorithm was used to extract 250 flexible gap motifs from the Prosite dataset entry PS00034 (55 sequences). The characteristics of the reported motifs (consider the definition […]


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