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At Molecular Station Bioinformatics, you will find all the bioinformatics programs you will need. To molekularnu kolodvor bioinformatiku, naći ćete sve bioinformatika programa trebat će vam. We have over 800 bioinformatic tools for DNA bioinformatics, RNA bioinformatics, Protein Bioinformatics, and Proteomic bioinformatic tools. Mi imamo preko 800 bioinformatika alata za bioinformatika DNA, RNA bioinformatici, protein bioinformatiku, i Proteomic bioinformatika alata. We also provide databses for each of these categories in order to easily find your sequence of interest from several sequence databases. Mi isto tako osigurati databses za svaku od tih kategorija, kako bi se lako pronaći svoj interes slijed od nekoliko slijed baza podataka.

Our Bioinformatic tools database has all the bioinformatic tools you will ever need and includes online programs and tools on: Naš bioinformatika alata za baze podataka ima sve bioinformatika alate koje ćete ikada trebati i uključuje online programa i alata na:

Latest Published Bioinformatics Articles from Entrez-Pubmed Journals Latest Published Articles bioinformatiku iz Entrez-Pubmed Časopisi

Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies. Multimarker analiza i okrivljavanje za više platformi ujedinjavanje-based genom-wide asocijacijske studije.

Bioinformatics. Bioinformatika. 2008 Jul 10; 2008 Srpanj 10;

Authors: Homer N, Tembe WD, Szelinger S, Redman M, Stephan DA, Pearson JV, Nelson SF, Craig D Autorstvo: Homer N, Tembe WD, Szelinger S, M Redman, Stephan DA, Pearson JV, Nelson SF, Craig D

SUMMARY: For many genome-wide association (GWA) studies individually genotyping one million or more SNPs provides a marginal increase in coverage at a substantial cost. SAŽETAK: Za mnoge genom-wide udruge (GWA) studija individualno genotipizacija milijun ili više SNPs pruža marginal povećanje pokrivenosti i znatan trošak. Much of the information gained is redundant due to the correlation structure inherent in the human genome. Velik dio informacija dobio je suvišan s obzirom na povezanost struktura inherent u ljudski genom. Pooling based GWA studies could benefit significantly by utilizing this redundancy to reduce noise, improve the accuracy of the observations, and increase genomic coverage. Ujedinjavanje temelji GWA studije mogli imati koristi znatno pomoću ovog zalihost za smanjenje buke, poboljšanje točnosti, promatranjima, kao i povećati pokrivenost genocid. We introduce a measure of correlation between individual genotyping and pooling, under the same framework that r(2) provides a measure of linkage disequilibrium between pairs of SNPs. Mi predstavljamo mjera korelacija između pojedinih genotipizacija i udruživanje, prema istom okviru koje r (2) pruža mjera povezivanja između parova disequilibrium of SNPs. We then report a new non-haplotype multimarker multi-loci method that leverages the correlation structure between SNPs in the human genome to increase the efficacy of pooling based GWA studies. Mi smo tada izvješće novi non-haplotype multimarker multi-Loci metoda pomoću koje je korelacija između strukture SNPs u ljudski genom kako bi povećali učinkovitost udruživanje zasniva GWA studija. We first give a theoretical framework and derivation of our multimarker method. Mi smo prvi dati teorijski okvir i izvor našeg multimarker metoda. Next, we evaluate simulations using this multimarker approach in comparison to single marker analysis. Zatim smo procijeniti simulacije pomoću ovog multimarker pristup u odnosu na jednu marker analysis. Finally, we experimentally evaluate our method using different pools of HapMap individuals on the Illumina 450S Duo, Illumina 550K, and Affymetrix 5.0 platforms for a combined total of 1,333,631 SNPs. Konačno, mi experimentally ocijenite naš način korištenjem različitih bazena, HapMap pojedinaca na Illumina 450S Duo, Illumina 550K, i Affymetrix 5,0 platforme za kombinirani ukupno 1333631 SNPs. Our results show that use of multimarker analysis reduces noise specific to pooling based studies, allows for efficient integration of multiple microarray platforms, and provides more accurate measures of significance than single marker analysis. Naši rezultati pokazuju da korištenje multimarker analiza smanjuje buku specifične za udruživanje zasniva studija, omogućava efikasna integracija više microarray platforme, i pruža više točne mjere od značaja od jednog marker analysis. Additionally, this approach can be extended to allow for imputing the association significance for SNPs not directly observed using neighboring SNPs in linkage disequilibrium. Osim toga, ovaj pristup može biti produžen do dopustiti za imputing udruge značaja za SNPs nije direktno opažena koristeći susjednog SNPs u vezni disequilibrium. This multimarker method can now be used to cost-effectively complete pooling-based GWA studies with multiple platforms across over one million SNPs and to impute neighboring SNPs weighted for the loss of information due to pooling. Ova metoda multimarker sada se može koristiti za cijenu učinkovito potpunu ujedinjavanje-based GWA studija sa mnogostruk platforma, preko više od milijun SNPs i okrivljuje susjednog SNPs ponderirana za gubitak informacije zbog udruživanje. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Dodatne informacije: Supplementary podaci su dostupni na bioinformatiku online.

PMID: 18617537 [PubMed - as supplied by publisher] PMID: 18617537 [PubMed - kao dobivenim od izdavača]

Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. CMT procjenu stanične linije stabilnosti po dva dimenzionalan gel-elektroforeza i masena spektrometrija temelji proteome analysis.

J Proteomics. J proteomike. 2008 Jul 21;71(2):160-167 2008 Srpanj 21, 71 (2) :160-167

Authors: Zhang K, Wrzesinski K, Fey SJ, Mose Larsen P, Zhang X, Roepstorff P Autorstvo: Zhang K, K Wrzesinski, Fey SJ, Mose Larsen P, Zhang X, Roepstorff P

Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) followed by mass spectrometric identification of the proteins in the protein spots has become a central tool in proteomics. Dvodimenzionalna gel-elektroforeza (2-D PAGE) i nakon toga mass spectrometric identifikaciju proteina i proteina u spotovima je postala centar alat u proteomics. CMT167(H), CMT64(M) and CMT170(L) cell lines, selected from a spontaneous mouse lung adenocarcinoma, with high-, middle- or low-metastatic potential have been characterized in vivo. CMT167 (H), CMT64 (M) i CMT170 (L) stanica linije, odabranih iz spontane miš Adenokarcinom pluća, s visoko, srednje ili low-metastatic potential su karakteriziraju in vivo. In this study, the comprehensive protein expression profiles of the CMT cell lines were analyzed at passages 5, 15 and 35 in order to assess the cell line stability. U ovom istraživanju, na sveobuhvatan protein expression profili od CMT stanične linije su analizirani i prolaza 5, 15 i 35 u cilju utvrđivanja cell line stabilnosti. During the passages 5 to 15, the expression profiles of CMT cells remained reasonably stable as evidenced by only 0.7%, 3.9% and 1.1% proteins changed in CMT167(H), CMT64(M) and CMT170(L) respectively. Tijekom prolaza od 5 do 15, izraz profile CMT stanica ostao je razumno stabilna kao što pokazuje samo 0,7%, 3,9% i 1,1% proteina promjena u CMT167 (H), CMT64 (M) i CMT170 (L) odnosno. However, the number of differentially expressed proteins were considerably increased at passage 35 in CMT64(M) and CMT170(L) while CMT167(H) remained stable. Međutim, broj differentially izrazio proteini su znatno povećana na 35 prolaz u CMT64 (M) i CMT170 (L), dok CMT167 (H) ostao stabilan. Based on our selection criteria, 22, 109 and 84 spots in CMT167(H), CMT64(M) and CMT170(L) were selected for protein identification by MS and 99 unique proteins were identified. Na temelju kriterija za odabir, 22, 109 i 84 mjesta u CMT167 (H), CMT64 (M) i CMT170 (L) su odabrani za identifikaciju proteina po MS i 99 jedinstvene bjelančevine su identificirali. Bioinformatics analysis indicated that most of these proteins participate in cellular metabolism. Bioinformatika analiza naznačeno da je većina od tih proteina sudjelovati u stanični metabolizam. In conclusion, proteomics was found to be a useful tool for assessing differences in cell line stability. U zaključku, proteomics je pronašao biti koristan alat za procjenu razlike u stanične linije stabilnosti. This approach provided a tool to select the best cell line and optimal subculture period for studies of cancer related phenomena and for testing the effect of potential anticancer drugs. Ovaj pristup pruža alat za odabir najbolje cell line Subculture i optimalno razdoblje za istraživanja raka u svezi fenomena i za testiranje i učinak potencijalnih antitumorski lijekovi.

PMID: 18617143 [PubMed - as supplied by publisher] PMID: 18617143 [PubMed - kao dobivenim od izdavača]

The Genome Sequencer FLXtrade mark System-Longer reads, more applications, straightforward bioinformatics and more complete data sets. The Genome usklađivač FLXtrade mark System-duži reads, više aplikacija, neposredan bioinformatika i potpunije setovi podataka.

J Biotechnol. J Biotechnol. 2008 Jun 21; 2008 Lipanj 21;

Authors: Droege M, Hill B Autorstvo: Droege M, B Hill

The Genome Sequencer FLX System (GS FLX), powered by 454 Sequencing, is a next-generation DNA sequencing technology featuring a unique mix of long reads, exceptional accuracy, and ultra-high throughput. The Genome usklađivač FLX System (GS FLX), powered by 454 po redu, je sljedeći-stvaranje sekvenciranje DNA tehnologiji koji sadrži jedinstvenu kombinaciju dugo čita, izuzetna preciznost, i ultra-visoke propusnosti. It has been proven to be the most versatile of all currently available next-generation sequencing technologies, supporting many high-profile studies in over seven applications categories. To je dokazano da je najkompletnija svih trenutno je dostupan sljedeći-stvaranje redoslijed tehnologije, s podrškom za mnoge visoke profil studija u više od sedam aplikacija kategorije. GS FLX users have pursued innovative research in de novo sequencing, re-sequencing of whole genomes and target DNA regions, metagenomics, and RNA analysis. GS FLX korisnici su progonili inovativna istraživanja u de novo sekvenciranje, re-sekvenciranje cijeloga genoma i ciljne DNA regija, metagenomics, i analiza RNA. 454 Sequencing is a powerful tool for human genetics research, having recently re-sequenced the genome of an individual human, currently re-sequencing the complete human exome and targeted genomic regions using the NimbleGen sequence capture process, and detected low-frequency somatic mutations linked to cancer. 454 redoslijed je moćan alat za humanu genetiku istraživanja, nakon što je nedavno re-poredan u genom od pojedinačnih ljudskih, trenutno re-sekvenciranje kompletan ljudskih exome genocid i ciljane regije koristeći NimbleGen sequence capture proces, a otkrivena je low-frequency somatske mutacije povezane do raka.

PMID: 18616967 [PubMed - as supplied by publisher] PMID: 18616967 [PubMed - kao dobivenim od izdavača]

[Prediction of outer membrane proteins using support vector machine with combined features] [Prediction of outer membranskih proteina korištenjem support vektorski stroj u kombinaciji sa značajkama]

Sheng Wu Gong Cheng Xue Bao. Sheng Wu GONG-Cheng Xue Bao. 2008 Apr;24(4):651-8 Travanj 2008, 24 (4) :651-8

Authors: Zou L, Wang Z, Wang Y Autorstvo: Zou L, Wang Z, Wang Y

Outer membrane proteins (OMPs) are embedded in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Vanjska membranski proteini (OMPs) su smjesteni u outer membrane of Gram-negativne bakterije, mitochondria, i chloroplasts. The cellular location and functional diversity of OMPs makes them an important protein class. Na stanični lokaciji i funkcionalna raznolikost OMPs ih čini važan protein klase. Researches on prediction of OMPs by bioinformatics methods can bring helpful methodologies for identifying OMPs from genomic sequences and for the successful prediction of their secondary and tertiary structures. Istraživanja na predviđanja od OMPs by bioinformatika metode može donijeti korisne metodologije za identificiranjem OMPs iz genocid sekvence i za uspješno predviđanje njihovih sekundarna i tercijarna struktura. In this paper, three feature classes were calculated from protein sequences: amino acid compositions, dipeptide compositions and weighted amino acid index correlation coefficients. U ovom radu, tri značajke klase su izračunata iz sekvenci proteina: aminokiselina kompozicije, dipeptid kompozicije i težinski aminokiselinskih indeksa koeficijenti korelacija. Then, three feature classes were combined and inputted into a support vector machine (SVM) based predictor to identify OMPs from other folding types of proteins. Zatim, tri značajke klase su u kombinaciji i inputted u vektor support machine (SVM) temelji se predviđač identificirati OMPs iz drugih folding vrste proteina. The results of discrimination using several combined features including four amino acid index categories were calculated, and the influence on discrimination accuracy using different correlation coefficients with different orders and weights was discussed. Rezultati diskriminacija koristi u kombinaciji nekoliko mogućnosti, uključujući četiri aminokiseline indeks kategorija, obračunati su i utjecaj na točnost diskriminacije korištenjem različitih koeficijenti korelacije s različitim naređenja i težine je objašnjeno. In cross-validated tests and independent tests for identifying OMPs from a dataset of 1087 proteins belonging to all different types of globular and membrane proteins, the method using combined features obtains an overall accuracy of 96.96% and 97.33% respectively. U cross-validated testovi i testovi za nezavisne identifikacije OMPs iz podataka za 1087 proteini pripadaju sve različite vrste globular i membranski proteini, metoda pomoću značajke kombinaciji dobije ukupni točnost od 96,96% i 97,33% odnosno. And these results outperform that of other methods in the literature. I ove rezultate Nadjačati da od drugih metoda u književnosti. Using this method, high specificities are shown from the results of identifying OMPs in five bacterial genomes, and over 99% OMPs with known three-dimensional structures in the PDB database are correctly discriminated. Koristeći ovu metodu, visoke posebnosti prikazane su od rezultata utvrđivanja OMPs u pet genoma bakterija, i preko 99% OMPs s poznatim trodimenzionalni strukture u PDB baza podataka ispravno su diskriminirani. These results indicate that the method is a powerful tool for OMPs discrimination in genomes. Ovi rezultati ukazuju da je metoda je snažan alat za OMPs diskriminacije u genocid.

PMID: 18616178 [PubMed - in process] PMID: 18616178 [PubMed - u procesu]

[Rapid detection of Pseudomonas aernginosa by the fluorescence quantitative TaqMan PCR assay targetting ETA gene] [Rapid detection of Pseudomonas aernginosa po fluorescencija TaqMan kvantitativna PCR esej ciljanje ETA gena]

Sheng Wu Gong Cheng Xue Bao. Sheng Wu GONG-Cheng Xue Bao. 2008 Apr;24(4):581-5 Travanj 2008, 24 (4) :581-5

Authors: Xiao X, Zhang J, Gong J, Pan Y, Yu Y, Yang X, Wu H Autorstvo: Xiao X, Zhang J, J GONG-a, Pan Y, Yu Y, X Yang, Wu H

Pseudomonas aernginosa (PA) is one of the most universal pathogens in clinical diagnosis, and conventional detection assay has many disadvantages. Pseudomonas aernginosa (PA) je jedna od najpoželjnijih univerzalni patogeni u kliničkoj dijagnozi, ali i konvencionalnoj detekciji esej ima mnogo nedostataka. In this research, a pair of specific primers and a TaqMan fluorescent probe were designed in the conservative region of ETA gene by the method of bioinformatics analysis, the detection method for PA was successfully developed. U ovom istraživanju, par specifične početnice i TaqMan fluorescencija probe su bile namijenjene u regiji ETA konzervativne gene od metoda bioinformatika analiza, metode za otkrivanje PA je uspješno razvio. Different gradient concentrations of PA DNA and various pathogen DNA were amplified by fluorescence quantitative PCR (FQ-PCR) to confirm the specificity and sensitivity of the developed method. Razni gradijenta koncentracije PA DNA i razne pathogen DNA su pojačan by fluorescencija kvantitativne PCR (FQ-PCR) da biste potvrdili specifičnost i osjetljivost na razvijena metoda. Results showed that the developed detection assay is more sensible and specific by comparison to the conventional FQ-PCR method, and it is valuable for research and application prospects. Rezultati su pokazali da su razvili otkrivanje esej je više osjetljiv i specifičan u odnosu na konvencionalan FQ-PCR metode, i to je vrijedna za istraživanje i primjena projektima.

PMID: 18616166 [PubMed - in process] PMID: 18616166 [PubMed - u procesu]