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May 2. 01. 4; Accepted 1. June 2. 01. 4; Published 2. June 2. 01. 4Copyright . This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR- associated protein (Cas) system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user- friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online. Introduction. Genome editing is a very useful technology in the research areas related to the functional genomics. Programmable nucleases like zinc finger nucleases (ZFN) and transcription activator- like effector nucleases (TALEN) are well known tools for targeted genome editing . Similarly, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR- associated protein (Cas) system enables genome engineering in animals and plants . This is an RNA guided system, which consists of a short guide RNA (g. RNA) and a Cas. 9 protein. The g. RNA contains 2. DNA sequence (known as spacer) that binds to the complementary strand of the target DNA by base- pairing and 7. The g. RNA interacts with Cas. The complex binds to the target sequence by base- pairing and cleaves ds. DNA at a specific position . A short conserved motif . Some off- target binding of the system is reported . Besides ds. DNA cleavage, the CRISPR- Cas system has been recently modified for nicking and repression of gene activity . It is reported as an effective tool for activation of gene expression also . Due to these novel features, this system is going to play very important role in genome engineering programs. Therefore, a dedicated tool for determination of specific CRISPR- Cas target sites is an utmost requirement for several research groups. Although detection of CRISPR- Cas target site is simple, which needs direct analysis of DNA sequences for the presence of specific 2. A few tools like CRISPR Design (http: //www. Further, these are web based tools that depend upon internet connectivity. 191160 - tumor necrosis factor; tnf - tumor necrosis factor, alpha; tnfa;; cachectin;; tnf, monocyte-derived;; tnf, macrophage-derived - tnf. This section presents the requirements for programs in: Biochemistry B.Sc. Honours; Computational Biochemistry B.Sc. Honours; Biochemistry B.Sc. Major; Requirements for the program Biochemistry and Biotechnology are presented.
Some of the tools like CRISPR design (http: //crispr. See Supplementary Table 1 in Supplementary Material available online at http: //dx. Therefore, a simple, easy to edit, and high throughput computational tool is required for the analysis of large datasets on the local machine. Here, we present SSFinder, a freeware written in python to find specific CRISPR- Cas target sites in limited time on even a personal computer. It is an organism independent freeware available at https: //code. MIT license. 2. Materials and Methods. The SSFinder is a Python script and can execute in Windows, Mac OS, and Linux operating systems. It is a low memory request tool, which enables the finding of specific CRISPR- Cas target sites. It can be installed on both personal computers and parallel computing system commonly known as . It only needs a compatible version of Python (2. A flow chart showing algorithm of the SSFinder is given in Figure 1. The DNA sequence is first analyzed for the occurrence of 2. These segments are further screened for the presence of 1. To further simplify, selected sequences are again classified into four groups on the basis of the start and end nucleotides, which are (1) G/C N7. S1. 1 G/C, (2) G/C N7. S1. 1 A/T, (3) A/T N7. S1. 1 A/T, and (4) A/T N7. S1. 1 G/C (N denotes for any nucleotides and S for seed sequences). Figure 1: A flow chart showing algorithm of the SSFinder for CRISPR- Cas target site prediction. To use SSFinder, users need to download the script or copy- paste the script in a notepad and save as . A working directory containing input file of FASTA formatted nucleotide sequences is also required. Finally, SSFinder can be executed by using the following command line in Linux terminal. User needs to provide an address of working directory, file name of input sequences, and desired output format (like. The output file will be saved automatically in the same directory with the file name . Sequences from the 7th column can be directly used as spacers in the g. RNA designing. Table 1: An overview of output file given by SSFinder. Figure 2: An overview of command prompt for using SSFinder in Windows operating system. Results and Discussion. The SSFinder facilitates prediction of CRISPR- Cas target sites in small as well as large genomic data. It is freeware for the researchers and can also be used on personal computers of any configuration. Compatibility with operating systems like Windows, Mac OS, and Linux makes this tool user- friendly for the researcher from nonbioinformatics background as well. The SSFinder scans a DNA sequence by moving a window of 2. Since the seed sequence determines the specificity of the CRISPR- Cas system . Sequences having distinct seed sequence in entire input sequence file are displayed in output file as specific target sites. Sometimes researchers need to target the genomic region start and end with specific nucleotide (like A/T/G/C). Therefore, the selected slices are further classified into four different motifs to ease the process. To test the performance of SSFinder, we used two types of large datasets: (1) multiple sequences with cumulative big size (2. Arabidopsis thaliana protein coding genes of ~3. TAIR1. 0, ftp: //ftp. Sequences/blast. In the first dataset, a total of 1. CRISPR- Cas binding. The result was in agreement with the earlier report . In case of second dataset, a total of 1. The analyzed data can be available on request. The average speed of the analysis was 3. The average distance between two specific target sites was 2. The results indicated that the SSFinder is a high throughput tool for CRISPR- Cas target site prediction from large datasets in limited time. Conclusion. We report SSFinder, a comprehensive tool for the identification of specific CRISPR- Cas target sites with high reliability. It is a freeware, easy to edit, and low memory demand tool compatible with many commonly used operating systems. Our tool is very useful in high throughput inhouse screening applications of large genomes in limited time. This can accelerate the functional genomics research based on the application of CRISPR- Cas system. Availability. The SSFinder is a python script, freely available at https: //code. Conflict of Interests. The authors declare that there is no conflict of interests regarding the publication of this paper. Authors. Shailesh Sharma developed the script and performed the experiment. Santosh Kumar Upadhyay and Shailesh Sharma contributed equally to this work. Acknowledgments. Authors are thankful to the National Agri- Food Biotechnology Institute (NABI), Mohali, India, for the research facility. Santosh Kumar Upadhyay is thankful to Department of Science and Technology (DST), Government of India, for DST INSPIRE Faculty Fellowship. 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Stakeholders provide or. Document Type: Project Overview Document <All project documents should be put under change management on initial creation> Author: <author’s name> Page 3 of 4 Printed: 09/04/2003 12:16. Project Summary Document Template. Project Overview Template WordArchaeology Data Service: Research. Semantic Technologies Enhancing Links and Linked data for Archaeological Resources. Arts & Humanities Research Council. For the management of features at the scale of a particular archaeological site. AHRC). STELLAR built on outcomes and tools from the previous AHRC funded. EPSRC funded. project, a collaboration with the Science Museum. To this end, third party data providers will use the tools developed by the project to map and extract archaeological datasets into RDF/XML representation conforming to the CIDOC CRM- EH standard ontology. These datasets will be generated as Linked Data. Evaluation will consider both the mapping and linked data generation exercises, taking account of technical and pragmatic issues. The following datasets were downloaded from the Channel Tunnel Rail Link (CTRL) excavation archive ( Stuart Foreman (2. Channel Tunnel Rail Link Section 1 . York: Archaeology Data Service . All of these databases included information typical of an excavation archive – stratigraphic (context/entity/group), small finds, event and environmental sampling tables – that it was hoped would be useful case- studies for the STELLAR tool. In addition, several other datasets were also downloaded. The next phase of work was undertaken using the STELLAR console. The resulting tables – conforming to the CRM- EH – were thus automatically exported to CSV, for example “hartshill. In each case it was mapped to the ADS’ Linked Data page. Hartshill was given the namespace: http: //data. ADS/DOI/1. 0. 5. 28. The CTRL datasets had the same doi, so were made unique by extending the string to include the individual site, for example: http: //data. ADS/DOI/1. 0. 5. 28. Once these steps had been completed – each individual CSV was exported to RDF. Digital Antiquity supports archaeological research, resource management. Following a guiding STAR? Latest EH work with, and plans for, Semantic Technologies Presented by Keith May Based on research work of English Heritage staff. Arachne is intended to provide archaeologists and Classicists with a free internet research tool for quickly. URIs (Universal Resource. The paper deals with the management of archaeological data from excavations that cannot be easily processed using traditional forms and relational databases. The STELLAR Project Semantic Technologies Enhancing Links and Linked data for Archaeological Resources Overview STELLAR was a 1 year project funded by the Arts. Integrating Terminological Tools and Semantic Archaeological Information: the ICCD RA Schema and Thesaurus. Negation detection and word sense disambiguation in digital archaeology reports for the purposes of semantic annotation.Il ritorno del mio Casio BM- 1. WJHo piacere di condividere con voi la storia di uno dei miei orologi, un vecchio e carissimo (sentimentalmente parlando) Casio BM- 1. WJ. Questo orologio e’ stato il primo ad incorporare un sensore di pressione, o in altre parole e’ l’antenato dei moderni Pro. Trek. La sua vendita inizio’ nel 1. Casio, tra i “milestone”: Dicevo.. Veramente notevole e’ il fatto che il sensore poteva anche funzionare come profondimetro! Early Casio Watches With Sensor data, Casio Record Data, Vintage Casio Stopwatches. Rare Casio Sensor Based Watches. DataBank/Calculator Watches. Casio Color Catalouge 1984. Vintage Casio Ladies Watches. Step-by-step instructions on how to change the battery on a Casio AMW-320R watch. Please give me a thumbs up if you found this useful! Skip navigation Upload. Yeah, keep it Undo Close. Sono veramente pochi, che io sappia, gli orologi con questa combinazione di alti/profondimetro, ad esempio: Citizen Aquamount, Casio SPF- 6. Suunto. Oltre alla referenza BM- 1. WJ, c’era anche quella (meno diffusa) BM- 1. J che era per il mercato USA e UK (es. Vi erano inoltre le seguenti versioni: tutto nero (il primo); nero con tasti gialli (probabilmente il piu’ diffuso); nero con tasti gialli e mascherina frontale (copri- sensore) anch’essa gialla (per il mercato interno); verde scuro con tasti neri. Vi era una sola versione di cinturino. Nel luglio del 1. BM- 1. 00. WJ (versione all- black), ed ero contentissimo Ho sfruttato questo orologio da nerd ed esploratore- alpinista fino al ’9. In quegli anni ero all’universita’ dove per la prima volta mi spiegarono cosa e’ e come funziona un semiconduttore. Nei successivi 1. Nel frattempo, le batterie morirono e il cinturino si decompose. Noooooo Volevo funzionante il mio BM- 1. WJ, proprio il mio e non un altro come il mio! Il primo tentativo fu quello di utilizzare il sensore di un altro orologio simile che ho, ovvero il BM- 6. HOla necesito por favor instrucciones para cambiar pilas y arrancar reloj CASIO 560 BM-100WJ con alt. Inventar el manual para entender las mujeres- Ir a tomar fotos a.Infatti il sensore e’ apparentemente identico nei due modelli. Il tentativo successivo fu quello di contattare il servizio tecnico della Casio, ma.. Infine decisi di contattare direttamente la sede principale (in giappone) della Fujikura, che e’ l’azienda che produceva e tutt’ora produce questi sensori a stato solido per la Casio. Scrissi e in meno di 2. Sfortunamente, mi scrisse, non c’e’ nulla che possono fare per aiutarmi. Letteralmente (copio- incollo): “I suppose you can not repair your watch by yourself even if you could change sensor part. Because each sensor needs the calibration process to match the sensor performance for LSI in the watch.” . Per poi finire con: “I believe you are good CASIO's customer and your watch is so happily that it was used for long time.” E’ molto giapponese, e’ un grande! Per completezza d’informazione, posto una foto di un sensore molto simile e del suo schema tecnico: Vabbe’, ricominciamo da capo, questa volta seguendo un’altra strategia.. Fortunamente, sono riuscito a trovare un altro vecchio BM- 1. WJ con modulo funzionante (cosi’ almeno mi era stato detto, anche se era rimasto con le batterie scariche da ormai diversi anni). In seguito, da un venditore ebay americano ho trovato il suo cinturino, ancora NOS (cosa tutt’altro che facile). Find great deals on eBay for Depth Meter in Wristwatches. Timex has detailed manual online. Simply Google 'T2N809 Manual'. Questo orologio e’ stato il primo ad incorporare un sensore di pressione, o in altre parole e’ l’antenato dei moderni ProTrek. La sua vendita inizio’ nel 1989, come anche specificato nel sito. PDF-MANUALS-DOWNLOAD-DOWNLOAD-PERKINS. Casio Watch Manual: Module 560 Next Page >> Next Page >> Full Listing of Casio Watch Modules and Manuals. Ball Breitling Casio Citizen Doxa Hamilton Invicta Omega Oris Panerai Rolex Seiko Sinn Suunto TAG Heuer Timex Zodiac. Casio ocw-520tde-1avef anleitung englisch. Solicitud de manual de cualquier propietario, libro de instrucciones, gu. Search English manuals CASIO 560 BM 100WJ > Search English manuals CASIO EFX 700 INSTRUCCIONES >. Nouveau moteur de recherche! Poi ho trovato una nuova guarnizione del fondello in un negozio vino casa! Dopo averla estratta ho visto che, per fortuna, era intatta. Ci ho messo un po’ di grasso al silicone, e via a rimontare il tutto.. Prima il sensore, poi il modulo, la nuova guarnizione e il fondello.. Aggiungo anche una foto del mio “nuovo” BM- 1. WJ insieme al mio ATC- 1. Per finire, IMHO.. Tutte le funzioni basiche erano e sono presenti. 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E LANIntegrated Realtek ALC8. HD audio. Up to 7. Support for S/PDIF out. Support for Dolby Home Theatre. Expansion slots. All PCI- E Express slots conform to the PCI- E 2. PCI- E x. 16 slot running at x. PCI- E x. 16 slot running at x. PCI- E x. 1 slots. PCI slots. ATX Form Factor; 3. CM x 2. 4. 4. CMRev 3. UEFI support with dual UEFI BIOSGigabyte GA- 9. A- DS3. AM3+ socket. Support for 3. 2nm AMD FX- Series 4- core, 6- core and 8- core processors (Bulldozer and Piledriver core)Support for existing AM3 Phenom II and Athlon II processors. VRM with no cooling, and 1. W CPU TDP support except FX- 8. XX (a notice about VRMs: it is highly recommended you ensure VRMs are cooled when overclocking any high wattage processor. For more info see hereand the notation in the questions & answers section below)Gigabyte Ultra Durable 4 Classic PCB4x 1. V DDR3 DIMM sockets supporting up to 3. GB of dual channel memory. Native support for DDR3 at 1. Mhz; can support higher mhz through overclocking. AMD 9. 70 northbridge chipset and AMD SB9. Support for AMD Crossfire. X at 1. 6X and 4. X using PCIEX1. 6 and PCIEX4 slots**Support for 6 SATA6. GB/s devices, as well as RAID0, RAID1, RAID5, RAID1. JBODUp to 1. 4 USB 2. USB)Up to 4 USB 3. Please note that a 4x PCI- E link will bottleneck graphics cards more powerful than an HD 5. Integrated Realtek RTL8. E LANIntegrated Realtek ALC8. HD audio. Up to 7. Support for S/PDIF out. Support for Dolby Home Theatre. Expansion slots. All PCI- E Express slots conform to the PCI- E 2. PCI- E x. 16 slot running at x. PCI- E x. 16 slot running at x. PCI- E x. 1 slots. PCI slots. ATX Form Factor; 3. CM x 2. 4. 4. CMRev 3. UEFI support with dual UEFI BIOSMembers list. People who want to submit for membership to the GA- 9. XA/9. 70. A- Series Owners Thread/Club may do so at . To be a verified owner (highlighted in orange), you must have a CPU- Z validation link, and must prove that your validation is stable (if overclocked) by providing a screenshot regarding stability in the thread. The screenshot may feature either Prime. Intel. Burn or Lin. X after 2. 0 passes on high, or OCCT for 3. As a unique feature of this club, we are allowing you to submit your info as a . However, we ask that all . The GA- 8. 70. A- UD3 uses the 8. There may be some design similiarities but the boards are not related. The GA- 8. 90. XA- UD3 is related to the Gigabyte 7. X series of boards. Note that while some of these boards may also boast an AM3+ socket or support running AM3+ processor otherwise, they will not support all features - a 9. Q: Will Crossfire. X or SLI at 8x bandwidth bottleneck anything vs. What about 4. X? A: 8x PCI- E will not bottleneck a video card from achieveing full performance unless you run a card as powerful or more powerful than an HD 6. GTX 5. 60, and with a very high reslution. PCI- E will begin to slightly bottleneck cards more powerful than the HD 6. A discrete graphics card is required to properly run your system with this motherboard. Q: In CPUID HWMonitor, which of the . For full information, see the section below labelled Shopping/pricing information. Q: Where can I download BIOS files for this board? A: BIOS files can be downloaded from the official Gigabyte website. If the latest version has bugs that affect your operation, try a later version. Q: When should I update my BIOS? A: It is recommended you update your BIOS only to support something that normally wouldn't be supported, or to fix a bug/problem with the current BIOS. Q: Where can I download driver files for this board? A: Drivers can be downloaded from the official Gigabyte website for this motherboard. Select the appropriate OS before downloading any drivers. For the GA- 9. 90. XA- UD3, . What does this mean? A: According to GIGABYTE, a Rev 1. Some boards may have major hardware changes. Q: Are BIOS version for . For the best compatibility you should visit the download BIOS page of your specific revision. You may wish to check the board label, there may be a sticker that denotes that it is a newer board with AM3+ out of the box support. Q: Why are the GA- 9. A- D3 and GA- 9. 70. A- DS3 generally not considered to be overclocking- ready? A: The GA- 9. 70. A- D3 and the GA- 9. A- DS3 use a lower count 4+1 phase VRM system with no heatsink cooling. You can usually get this revision at no extra cost if you ask the store about it. Prefer it if the store has it. Q: Is it possible to refit a Rev 1. GA- 9. 70. A- D3 with VRM heatsinks? A: There are VRM heatsink mounts that can take on a properly sized VRM heatsink or you can mount individual heatsinks. There have been known instances of GIGABYTE sending rev 1. VRM heatsink after asking - although some have been turned down this. Q: What is different with the Rev 3. A: The primary difference is that the Rev 3. UEFI instead of the traditional BIOS. Motherboard manual (online)For the GA- 9. XA- UD3, . The versions available are: FA BIOS - 2. First release - supports Vishera FX - support all socket AM3+ CPUs. Support new socket AM3+ FX CPUs: FX- 8. FX- 8. 32. 0, FX- 6. FX- 4. 30. 0GA- 9. XA- UD3- Rev 1. x (intercompatible)The BIOS files may be downloaded from the official Gigabyte website at . The versions available are: F1. BIOS - 2. 01. 2/1. Update CPU AGESA 1. BETA BIOS - updated to support all socket AM3+ CPUs. Support new socket AM3+ FX CPUs: FX- 8. FX- 8. 32. 0, FX- 6. FX- 4. 30. 0F1. 3b BIOS - 2. Update CPU AGESA 1. Update AHCI ROM 3. SSD compatibility - BETA BIOSF1. BIOS - 2. 01. 2/0. Modify ET6 Function. BUG FIXED: - Instability, very delayed startup with AMD FX processor - . Fixed with revert to F8. F8 BIOS - 2. 01. 1/0. Improves compatibility. Not known what is improved in terms of compatibility. F7 BIOS - 2. 01. 1/0. Improves stability. Slightly faster POST sequence. It may be downloaded by . The versions available are: FA BIOS - 2. First release - supports Vishera FX - support all socket AM3+ CPUs. Support new socket AM3+ FX CPUs: FX- 8. FX- 8. 32. 0, FX- 6. FX- 4. 30. 0GA- 9. A- UD3 - Rev 1. x (intercompatible)The BIOS files may be downloaded from the official Gigabyte website at . The versions available are: F7e BIOS - 2. Update CPU AGESA 1. BETA BIOS - updated to support all socket AM3+ CPUs. Support new socket AM3+ FX CPUs: FX- 8. FX- 8. 32. 0, FX- 6. FX- 4. 30. 0F7c BIOS - 2. Update CPU AGESA 1. Update AHCI ROM 3. SSD compatibility - BETA BIOSF6 BIOS - 2. Modify ET6 Function. F5. B BIOS - 2. 01. Modify CPU compatibility - BETA BIOSF5. B BIOS(no longer available) - 2. Support Quick Boost function - BETA BIOSF4 BIOS - 2. Update CPU AGESA 1. F3 BIOS - 2. 01. 1/0. Update CPU AGESA 0. AM3+ CPUs - Modified TPM compatibility. Support these socket AM3+ FX CPUS: FX- 4. W, FX- 6. 10. 0 9. W, FX- 8. 10. 0 9. W, FX- 8. 12. 0 9. W, FX- 8. 12. 0 1. W, FX- 8. 15. 0 1. WF1 BIOS - 2. 01. First release. GA- 9. A- D3 - Rev 3. 0 (UEFI equipped)The BIOS files may be downloaded from the official Gigabyte website at . The versions available are: FA BIOS - 2. First release - supports Vishera FX - support all socket AM3+ CPUs. Support new socket AM3+ FX CPUs: FX- 8. FX- 8. 32. 0, FX- 6. FX- 4. 30. 0GA- 9. A- D3. Rev 1. 3- 1. The BIOS files may be downloaded from the official Gigabyte website at . The versions available are: FB BIOS - 2. First release - supports Vishera FX - updated to support some socket AM3+ CPUs. Limited support for new socket AM3+ FX CPUs: FX- 6. FX- 4. 30. 0 - NO 1. W TDP FX- 8. 3XX SUPPORTGA- 9. A- DS3 - Rev 1. x (intercompatible)The BIOS files may be downloaded from the official Gigabyte website at . The versions available are: F5 BIOS - 2. Update CPU AGESA 1. AM3+ CPUs. Limited support for new socket AM3+ FX CPUs: FX- 6. FX- 4. 30. 0 - NO 1. W TDP FX- 8. 3XX SUPPORTF4 BIOS - 2. Update CPU AGESA 1. Update AHCI ROM 3. Improve SSD compatibility. F3 BIOS - 2. 01. 2/0. GA- 9. 70. A- DS3 1. Release BIOS - Modify VGA card compatibility. F2 BIOS - 2. 01. 2/0. Update CPU AGESA 1. F1 BIOS - 2. 01. 2/0. First release. Memory support information. To view the memory support list for the GA- 9. XA- UD3, . Shopping/pricing information. Best deal for the GA- 9. XA- UD3 (last updated 2. March, 2. 01. 2). Best deal for the GA- 9. A- UD3 (last updated 2. December 2. 01. 1)Best deal for the GA- 9. A- D3 (last updated 2. Dec 2. 01. 1). * Many Canadian stores offer price match service; if a certain store is closer to you/local, you may be able to price match to this online store there and pick up rather than pay shipping.** Indicates that the rebate offers the no- wait rebate service. For an extra $2 deducted from rebate check, you can have the rebate processing sped up so that the check returns to you in 9 days - as opposed to the usual 8- 1. Indicates that this choice may be cheaper if buying locally (i. NOTICE: It is recommend that permanent overclocking be done in the BIOS, not with software! Monitoring tools. |
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