scholarly journals Analysis of Generalized Pattern Searches

2006 ◽  
Author(s):  
Charles Audet ◽  
J. E. Dennis Jr
Keyword(s):  
Pattern Searches

scholarly journals Compact and hash based variants of the suffix array

2017 ◽  
Vol 65 (4) ◽  
pp. 407-418
Author(s):  
S. Grabowski ◽  
M. Raniszewski
Keyword(s):  
Data Structure ◽  
Full Text ◽  
Hash Table ◽  
Suffix Array ◽  
Fixed Size ◽  
Text Indexing ◽  
Text Length ◽  
Speed Up ◽  
Pattern Searches ◽  
Search Interval

AbstractFull-text indexing aims at building a data structure over a given text capable of efficiently finding arbitrary text patterns, and possibly requiring little space. We propose two suffix array inspired full-text indexes. One, called SA-hash, augments the suffix array with a hash table to speed up pattern searches due to significantly narrowed search interval before the binary search phase. The other, called FBCSA, is a compact data structure, similar to Mäkinen’s compact suffix array (MakCSA), but working on fixed size blocks. Experiments on the widely used Pizza & Chili datasets show that SA-hash is about 2–3 times faster in pattern searches (counts) than the standard suffix array, for the price of requiring 0.2n–1.1nbytes of extra space, wherenis the text length. FBCSA, in one of the presented variants, reduces the suffix array size by a factor of about 1.5–2, while it gets close in search times, winning in speed with its competitors known from the literature, MakCSA and LCSA.

The ETCBC Database of the Hebrew Bible

2018 ◽  
Vol 27 (1) ◽  
Author(s):  
Cody Kingham ◽  
Wido Van Peursen
Keyword(s):  
Hebrew Bible ◽  
Dead Sea Scrolls ◽  
Dead Sea ◽  
Function Approach ◽  
Searchable Database ◽  
Surface Level ◽  
Research Questions ◽  
Pattern Searches

We provide a brief introduction to the history, methodology, and tools of the Eep Talstra Centre for Bible and Computer (ETCBC). The ETCBC maintains a searchable database of morphology, syntax, and text-level features for the Hebrew Bible, Hebrew inscriptions, Dead Sea Scrolls, the Peshitta, and one of the Targumim. The ETCBC follows a form-to-function approach, in which surface-level features are registered first and functional labels second. Linguists and exegetes can use the database’s freely accessible query tools for pattern searches and analysis of the text’s structure to address their research questions

HANDWRITTEN DIGIT RECOGNITION USING TWO-LAYER SELF-ORGANIZING MAPS

1994 ◽  
Vol 05 (04) ◽  
pp. 357-362 ◽  
Author(s):  
JING WU ◽  
HONG YAN ◽  
ANDREW CHALMERS
Keyword(s):  
Neural Network ◽  
New Method ◽  
Base Layer ◽  
Self Organizing Map ◽  
Handwritten Digit Recognition ◽  
Self Organizing Maps ◽  
Digit Recognition ◽  
Handwritten Digit ◽  
Pattern Searches ◽  
Self Organizing

In this paper, we present a two-layer self-organizing neural network based method for handwritten digit recognition. The network consists of a base layer self-organizing map and a set of corresponding maps in the second layer. The input patterns are partitioned into subspace in the first layer. Patterns in a subspace are led to the second layer and a corresponding map is built according to the first layer performance. In the classification process, each pattern searches for several closest nodes from the base map and then it is classified into a specified class by determining the nearest model of the corresponding maps in the second layer. The new method yielded higher accuracy and faster performance than the ordinary self-organizing neural network.

scholarly journals Analysis of Generalized Pattern Searches

2002 ◽  
Vol 13 (3) ◽  
pp. 889-903 ◽  
Author(s):  
Charles Audet ◽  
J. E. Dennis
Keyword(s):  
Pattern Searches

scholarly journals In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes

Marine Drugs ◽  
2020 ◽  
Vol 18 (9) ◽  
pp. 439
Author(s):  
Louis Benoist ◽  
Baptiste Houyvet ◽  
Joël Henry ◽  
Erwan Corre ◽  
Bruno Zanuttini ◽  
...  
Keyword(s):  
Immune Response ◽  
Antimicrobial Peptides ◽  
In Silico ◽  
De Novo ◽  
In Silico Analysis ◽  
Sepia Officinalis ◽  
Vibrio Splendidus ◽  
Pattern Searches ◽  
Sequence Characteristics ◽  
Silico Analysis

Cuttlefish (Sepia officinalis) haemocytes are potential sources of antimicrobial peptides (AMPs). To study the immune response to Vibrio splendidus and identify new AMPs, an original approach was developed based on a differential transcriptomic study and an in-depth in silico analysis using multiple tools. Two de novo transcriptomes were retrieved from cuttlefish haemocytes following challenge by V. splendidus or not. A first analysis of the annotated transcripts revealed the presence of Toll/NF-κB pathway members, including newly identified factors such as So-TLR-h, So-IKK-h and So-Rel/NF-κB-h. Out of the eight Toll/NF-κB pathway members, seven were found up-regulated following V. splendidus challenge. Besides, immune factors involved in the immune response were also identified and up-regulated. However, no AMP was identified based on annotation or conserved pattern searches. We therefore performed an in-depth in silico analysis of unannotated transcripts based on differential expression and sequence characteristics, using several tools available like PepTraq, a homemade software program. Finally, five AMP candidates were synthesized. Among them, NF19, AV19 and GK28 displayed antibacterial activity against Gram-negative bacteria. Each peptide had a different spectrum of activity, notably against Vibrio species. GK28—the most active peptide—was not haemolytic, whereas NF19 and AV19 were haemolytic at concentrations between 50 and 100 µM, 5 to 10 times higher than their minimum inhibitory concentration.

Sign in / Sign up

Export Citation Format

Share Document