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Sequence searching tools
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With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies.
17p
vilarryellison
29-10-2021
10
1
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Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes.
16p
viansan2711
30-07-2021
15
2
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HMMER is a commonly used bioinformatics tool based on Hidden Markov Models (HMMs) to analyze and process biological sequences. One of its main homology engines is based on the Viterbi decoding algorithm, which was already highly parallelized and optimized using Farrar’s striped processing pattern with Intel SSE2 instruction set extension.
13p
vikentucky2711
26-11-2020
10
1
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Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms.
12p
vikentucky2711
26-11-2020
8
0
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Evolutionary variations let us define a set of similar nucleic acid sequences as a family if these different molecules execute a common function. Capturing their sequence variation by using e. g. position specific scoring matrices significantly improves sensitivity of detection tools.
17p
vikentucky2711
24-11-2020
9
1
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Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools.
11p
vioklahoma2711
19-11-2020
10
1
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Next generation sequencing technology has enabled characterization of metagenomics through massively parallel genomic DNA sequencing. The complexity and diversity of environmental samples such as the human gut microflora, combined with the sustained exponential growth in sequencing capacity, has led to the challenge of identifying microbial organisms by DNA sequence.
12p
vioklahoma2711
19-11-2020
12
2
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PSI-BLAST, an extremely popular tool for sequence similarity search, features the utilization of PositionSpecific Scoring Matrix (PSSM) constructed from a multiple sequence alignment (MSA). PSSM allows the detection of more distant homologs than a general amino acid substitution matrix does.
8p
viflorida2711
30-10-2020
10
2
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Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species.
13p
viconnecticut2711
29-10-2020
4
1
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The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible nonpseudoknotted RNA structures for RNA sequences.
12p
viconnecticut2711
29-10-2020
10
2
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Growing concern about the emergence of antibiotic resistance is compelling the pharmaceutical industry to search for new antimicrobial agents. The availability of genome sequences has enabled the development of computational mining as an important tool in the discovery of natural products with antibiotic effect
10p
vicoachella2711
27-10-2020
13
0
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Genetic sequence database retrieval benchmarks play an essential role in evaluating the performance of sequence searching tools. To date, all phylogenetically diverse benchmarks known to the authors include only query sequences with single protein domains.
9p
vicoachella2711
27-10-2020
15
0
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During hypoxia, the hypoxia inducible factor (HIF) binds to hypoxiaresponse elements (HRE) and induces the expression of hypoxia-inducible genes (HIG). A functionally active HRE typically contains an adjacent hypoxia ancillary sequence (HAS) in its downstream within the space of 7- 15 nt.
7p
chauchaungayxua8
03-10-2020
8
2
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DNA barcoding is a useful tool for species identification and phylogenetic construction. We tested the genus/species identification and phylogenetic construction in three tropical medicinal plants such as P. corylifoilia, M. pruriens and C. ternatea using a universal chloroplast DNA barcode trnH-psbA. The trnH-psbA primer pairs were used to amplify 250 bp DNA fragment in all three genera. The barcode sequences were submitted on NCBI-BLAST search and showed the nucleotide sequence similarity (homology) of 96% with P. corylifolia, 100% with M. pruriens and with 77% C. ternatea.
8p
quenchua6
15-06-2020
7
1
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The fungus Venturia carpophila causes scab in almond. In order to gain insight, an in vitro culture of the fungus has been established and its identity confirmed by its nr DNA. Internal transcribed spacer-ribosomal DNA (ITS-rDNA); the fungal molecular marker was used for molecular analysis. The target region of rDNA (ITS1-5.8S-ITS2) of this species was amplified using universal fungal primers (ITS1 and ITS4).
7p
chauchaungayxua3
07-02-2020
12
1
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Minor millets are under-exploited plant species often dubbed as ‘Crops for the future’ as they are best adapted to less fertile area and can survive limited water situations and relatively free from pests and diseases. Degenerate oligo-PCR strategy was employed to isolate resistant gene analogues from minor millets by amplifying samples using NBSLRR gene specific primers. Genomic DNA was isolated from the young leaves of minor millets viz., Foxtail millet (Setaria italica) var. CO 5 and Finger millet (Eleusine corocana) var. CO (Ra) 14 by following CTAB method with minor modifications.
9p
nguaconbaynhay1
04-12-2019
12
0
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Jewels of Opar (Talinum paniculatum) is a herbaceous plant known for its highly medicinal value. This medicinal plant is listed in the Red List of Vietnam’s medicinal plants and in the handbook of Vietnam’s medicinal plants, both documents warranting its necessity for protection. Jewels of Opar contains bioactive substances such as phytosterols, saponins, flavonoids, tannins, steroids, and many other inorganic substances. Jewels of Opar plants collected in Thanh Hoa, Vietnam, are tree-like herbs, their green trunks grows straight up and then branch out.
4p
caygaocaolon1
13-11-2019
19
2
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Waxy genes of the original variety and its mutant type were sequenced by Sanger method and compared through Nucleotide Basic Local Alignment Search Tool (BLASTN) to clarify differences. BLASTN result showed four nucleotide mutations in coding regions and 59 nucleotide mutations in noncoding regions.
17p
vineptune2711
04-11-2019
14
2
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Glutamine synthetase (GS) is expressed at high levels in subsets of cells in some tissues and at low levels in all cells of other tissues, suggesting that the GS gene is surrounded by multiple regulatory elements.We searched for such elements in the 2.5-kbupstreamregionand in the 2.6-kbfirst intronof theGSgene, usingFTO-2Bhepatoma andC2/7muscle cells as representatives of both cell types and transient transfec-tion assays as our tools.
7p
tumor12
20-04-2013
34
2
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Perhaps the most widely used applications of bioinformatics are tools such as psi-blast for searching sequence databases. We describe a recently developed protein database search algorithm calledrankprop. rankprop relies upon a precomputed network of pairwise protein similarities. The algorithm performs a diffusion operation from a specified query protein across the protein similarity network.
10p
fptmusic
12-04-2013
46
1
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