Gapped

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If your contig sequences include runs of N's that represent gaps, you will need to include assembly_gap features with the appropriate linkage evidence. If the sequences meet certain requirements, then you can generate a gapped submission with tbl2asn (v 22.9 or higher, available from FTP ) using the arguments -l (to add linkage evidence) and -a (to add assembly_gaps), as described below. If you have multiple linkage types in a single sequence or if any of the gaps are between scaffolds, please contact us for additional instructions, as these simple instructions are not sufficient for those more complex cases.

  1. Gapped Up Stocks
  2. Gapped Teeth Before And After
  3. Gapped Front Teeth
  4. Gapped Clock
  5. Gapped Dna
  6. Air Gapping

Requirements

  • Each record must represent a sequence that occurs biologically in the organism. Do NOT manually use N's to randomly combine the contigs to create a single sequence; you must know the order and orientation of the contigs.
  • Do not include any artificial sequences, such as linkers with multiple stop codons in the submitted genome.
  • Do not add assembly_gaps for Ns that represent ambiguous base calls, so you may need to check the parameters of the assembler that was used to determine what the N's represent. To convert the runs of Ns to assembly_gaps, you need to know:
    • the linkage evidence for each gap
    • the minimum number of N's in a row (ie 'run of Ns') that represents a gap
    • if any runs of Ns represent gaps of unknown size
    • if the sequences also include N's that are ambiguous base calls, then what is the length of the longest run of ambiguous bases. To use these simple instructions, the maximum number of Ns in a row that are ambiguous bases must be less than the minimum number of N's in a row that represents a gap.
  • For these simple instructions, all the gaps must be within scaffolds and have the same linkage evidence; gaps of unknown size must be represented by 100 Ns; and all runs of 'ambiguous base Ns' must be shorter than any run of Ns that represents a gap. More complex cases such as those will require more detailed instructions, so contact us if the genome assembly is more complicated.

Definition of gapped in the Definitions.net dictionary. Meaning of gapped. What does gapped mean? Information and translations of gapped in the most comprehensive dictionary definitions resource on the web. The process of transferring assets to and from an air-gapped service, which is burdensome in traditional cold storage and disruptive to availability, is instead seamless and instant for clients signing transactions with Curv Air Gap. Multiple transactions can additionally be batched together.

Gap Details

There are two types of gap lengths:

  • Estimated length: The approximate gap size is known. This is also used if the gap is known to be small (e. g. gap could be between 10-50 N's).
  • Unknown length: The gap size is not known (e.g. gap could be 50 or 50000 N's) but the order and orientation of the contigs are known. We suggest using 100 N's to represent gaps of unknown length rather than a random number because it will allow you to add assembly_gap features using tbl2asn.

Use the -l argument (lowercase 'l' as in 'linkage') followed by the type of evidence used to assert linkage across the gaps. These are the available options (they correspond to the options for column 9 of an AGP file):

  • paired-ends (ie, for paired ends or mate pairs)
  • align-genus
  • align-xgenus
  • align-trnscpt (ie, the evidence is a transcript)
  • within-clone
  • clone-contig
  • map
  • strobe (ie, from PacBio)

Use the argument -a followed by r#k or r#u to define how to interpret the runs of Ns in the sequences.

Gapped
  • r# indicates the size of the minimum run of Ns to convert to a gap
  • k/u indicates whether all the gaps are of estimated length (=k) or if runs of 100 Ns represent gaps of unknown length (=u)

Common Cases

1. All the gaps are of estimated lengths, use -a r#k

The # indicates the size of the minimum run of N's to convert to an estimated length gap. For example, if all of the gaps are estimated length (there are no unknown length gaps) and runs of 5 or more N's are estimated gaps and shorter runs of N's are ambiguous bases, then use -a r5k. Similarly, if every N represents an estimated length gap, use -a r1k.

Example: Every run of 5 or more Ns represents a gap of estimated length, and the linkage evidence is paired-ends:

Gapped
  • tbl2asn -p path_to_fsa_files -t template -M n -Z discrep -a r5k -l paired-ends

Note that you should only include an assembly_gap for runs of N's that represent gaps. Do not add assembly_gaps for single or short runs of N's that represent ambiguous bases. You will need to check your assembly parameters to determine what the N's represent.

2. ALL of the gaps are 100bp and are of unknown length, use -a r100u

Note that all of the unknown length gaps must be 100 N's. An assembly_gap will be added for every run of 100 N's. All other N's will be ignored. Please contact us for additional instructions if there are unknown length gaps of other sizes.

Example: all gaps are 100 Ns and are of unknown length, and the linkage evidence is by alignment to another genome of the same genus:

  • tbl2asn -p path_to_fsa_files -t template -M n -Z discrep -a r100u -l align-genus

Note that you must know the order and orientation of the contigs. You cannot randomly link contigs using unknown (or known) length gaps. If you do not have linkage evidence, submit the sequences as individual contigs.

3. There are both estimated length and unknown length gaps, use -a r#u.

Note that all of the unknown length gaps must be 100 N's. The # indicates the size of the minimum number of N's to convert to an estimated length gap. If some run's of 100 N's are unknown length and others are estimated length, please contact us for more information.

Gapped Up Stocks

Example: if runs of 10 or more N's are estimated gaps, and shorter runs of N's are just ambiguous bases, and all runs of exactly 100 N's are unknown gaps, and the linkage evidence is paired-ends:

  • tbl2asn -p path_to_fsa_files -t template -M n -Z discrep -a r10u -l paired-ends

4. Complex cases

Gapped Teeth Before And After

There may be complex assemblies that cannot be appropriately represented by the above examples, eg the sequences are chromosomes and some of the gaps are between scaffolds, or there are different kinds of linkage evidences for the gaps within a sequence, or some runs of Ns of particular lengths within a sequence represent gaps but others of those lengths are ambiguous base calls. In these cases, please contact us for additional instructions.

Annotation FYI

Annotation is not required. However, if you would like to annotate the gapped sequences, you need to be careful about crossing gaps.

A CDS may not cross the gap if the gap size is unknown. Instead, you could have two partial CDS features (and mRNAs in eukaryoties) that abut the gap, with a single gene over the whole locus. Alternatively, one of the partial CDS/mRNA features may be deleted if it is very short and there is little or no supporting evidence. If you have a single gene and two partial CDS/mRNA features, you should: (1) add a note to each CDS referencing the other half of the gene, (2) add a note to the gene and CDS features stating, 'gap found within coding sequence.'

A CDS can cross the gap if the gap size is estimated; however, a CDS (or mRNA) should not cross a gap such that over 50% of the translation is X (ie, in the gap). This situation will generate an error. Again, the CDS/mRNA should either be partial up to the gap or split into two partial CDS/mRNA features on either side of the gap, depending upon your confidence in the translation on each side of the gap.

In addition, no feature should begin or end inside a gap. Instead, the feature should abut the gap and be partial.

For more information about splitting CDS features, see either the eukaryotic annotation guidelines or the prokaryotic annotation guidelines .

tbl2asn arguments

Genome Resources

An air gap, air wall, air gapping[1] or disconnected network is a network security measure employed on one or more computers to ensure that a secure computer network is physically isolated from unsecured networks, such as the public Internet or an unsecured local area network.[2] It means a computer or network has no network interfaces connected to other networks,[3][4] with a physical or conceptual air gap, analogous to the air gap used in plumbing to maintain water quality.

Use in classified settings[edit]

An 'air-gapped' computer or network is one that has no network interfaces, either wired or wireless, connected to outside networks.[3][4] Many computers, even when they are not plugged into a wired network, have a wireless network interface controller (WiFi) and are connected to nearby wireless networks to access the Internet and update software. This represents a security vulnerability, so air-gapped computers either have their wireless interface controller permanently disabled or physically removed. To move data between the outside world and the air-gapped system, it is necessary to write data to a physical medium such as a thumbdrive, and physically move it between computers. Physical access has to be controlled (man identity and storage media itself). It is easier to control than a direct full network interface, which can be attacked from the exterior insecure system and, if malware infects the secure system, can be used to export secure data. That's why some new hardware technologies are also available like unidirectional data diodes or bidirectional diodes (called also electronic airgap), that will cut physically the network and transportation layers, copy and filter the application data.

In environments where networks or devices are rated to handle different levels of classified information, the two disconnected devices or networks are referred to as 'low side' and 'high side', 'low' being unclassified and 'high' referring to classified, or classified at a higher level. This is also occasionally referred to as 'red' (classified) and 'black' (unclassified). Access policies are often based on the Bell–LaPadula confidentiality model, where data can be moved low-to-high with minimal security measures, while high-to-low requires much more stringent procedures to ensure protection of the data at a higher level of classification. In some cases (for instance industrial critical systems), the policy is different : data can be moved from high-to-low with minimal security measures, but low-to-high requires a high level of procedures to ensure integrity of the industrial safety system.

The concept represents nearly the maximum protection one network can have from another (save turning the device off). One way to transfer data between the outside world and the air-gapped system is to copy data on a removable storage medium such as a removable disk or USB flash drive and physically carry the storage to the other system. This access still has to be carefully controlled since USB drive may have vulnerabilities (see below). The upside to this is that such a network can generally be regarded as a closed system (in terms of information, signals, and emissions security), unable to be accessed from the outside world. The downside is that transferring information (from the outside world) to be analyzed by computers on the secure network is extraordinarily labor-intensive, often involving human security analysis of prospective programs or data to be entered onto air-gapped networks and possibly even human manual re-entry of the data following security analysis.[5] That's why another way to transfer data, used in appropriate situations like critical industries, is to use data diodes and electronic airgaps, that assure a physical cut of the network by a specific hardware.

Sophisticated computer viruses for use in cyberwarfare, such as Stuxnet[6] and agent.btz have been designed to infect air-gapped systems by exploiting security holes related to the handling of removable media. The possibility of using acoustic communication has also been demonstrated by researchers.[7] Researchers have also demonstrated the feasibility of data exfiltration using FM frequency signals.[8][9]

Gapped Front Teeth

Examples[edit]

Examples of the types of networks or systems that may be air gapped include:

  • Military/governmental computer networks/systems;[10]
  • Financial computer systems, such as stock exchanges;[11]
  • Industrial control systems, such as SCADA in Oil & Gas fields;[12]
  • Life-critical systems, such as:
    • Controls of nuclear power plants;
    • Computers used in aviation,[13] such as FADECs, air traffic control systems, and avionics;
    • Computerized medical equipment;
  • Very simple systems, where there is no need to compromise security in the first place, such as:
    • The engine control unit and other devices on the CAN bus in an automobile;
    • A digital thermostat for temperature and compressor regulation in home HVAC and refrigeration systems;
    • Electronic sprinkler controls for watering of lawns.

Many of these systems have since added features that connect them during limited periods of time to the organisation's internet (for the need of surveillance or updates) or the public internet, and are no longer effectively and permanently air gapped, including thermostats with internet connections and automobiles with Bluetooth, Wi-Fi and cellular phone connectivity.

Limitations[edit]

Limitations imposed on devices used in these environments may include a ban on wireless connections to or from the secure network, or similar restrictions on EM leakage from the secure network through the use of TEMPEST or a Faraday cage.

Despite a lack of direct connection to other systems, air-gapped networks have been shown to be vulnerable to attack in various circumstances.

Scientists in 2013 demonstrated the viability of air gap malware designed to defeat air gap isolation using acoustic signaling.[citation needed] Shortly after that, network security researcher Dragos Ruiu's BadBIOS received press attention.[14]

In 2014, researchers introduced 'AirHopper', a bifurcated attack pattern showing the feasibility of data exfiltration from an isolated computer to a nearby mobile phone, using FM frequency signals.[8][9]

In 2015, BitWhisper, a covert signaling channel between air-gapped computers using thermal manipulations was introduced. BitWhisper supports bidirectional communication and requires no additional dedicated peripheral hardware.[15][16]

Later in 2015, researchers introduced GSMem, a method for exfiltrating data from air-gapped computers over cellular frequencies. The transmission - generated by a standard internal bus - renders the computer into a small cellular transmitter antenna.[17][18]

ProjectSauron malware discovered in 2016 demonstrates how an infected USB device can be used to remotely leak data off of an air-gapped computer. The malware remained undetected for 5 years and relied on hidden partitions on a USB drive not visible to Windows as a transport channel between the air-gapped computer and a computer connected to the internet, presumably as a way to share files between the two systems.[19]

Gapped Clock

NFCdrip was the name given to the discovery of stealthy data exfiltration through NFC (Near-field communication) radio abuse and signal detection in 2018. Although NFC enables devices to establish effective communication by bringing them within a few centimeters of each other,[20] researchers showed that it can be abused to transmit information at a much longer range than expected - up to 100 meters.[21]

In general, malware can exploit various hardware combinations to leak sensitive information from air-gapped systems using 'air-gap covert channels'.[22] These hardware combinations use a number of different mediums to bridge the air-gap, including: acoustic, light, seismic, magnetic, thermal, and radio-frequency.[23][24][25]

See also[edit]

References[edit]

Gapped Dna

  1. ^'What is air gapping (air gap attack)?'. WhatIs.com. Retrieved 2020-12-16.
  2. ^Internet Security Glossary, Version 2. RFC4949.
  3. ^ abZetter, Kim (8 December 2014). 'Hacker Lexicon: What is an air gap?'. Wired magazine website. Conde Nast. Retrieved 21 January 2019.
  4. ^ abBryant, William D. (2015). International Conflict and Cyberspace Superiority: Theory and Practice. Routledge. p. 107. ISBN978-1317420385.
  5. ^Lemos, Robert (2001-02-01). 'NSA attempting to design crack-proof computer'. ZDNet News. CBS Interactive, Inc. Retrieved 2012-10-12. For example, top-secret data might be kept on a different computer than data classified merely as sensitive material. Sometimes, for a worker to access information, up to six different computers can be on a single desk. That type of security is called, in typical intelligence community jargon, an air gap.
  6. ^'Stuxnet delivered to Iranian nuclear plant on thumb drive'. CNET. 12 April 2012.
  7. ^Putz, Florentin; Álvarez, Flor; Classen, Jiska (2020-07-08). 'Acoustic integrity codes: secure device pairing using short-range acoustic communication'. Proceedings of the 13th ACM Conference on Security and Privacy in Wireless and Mobile Networks. Linz Austria: ACM: 31–41. arXiv:2005.08572. doi:10.1145/3395351.3399420. ISBN978-1-4503-8006-5. S2CID218673467.
  8. ^ abGuri, Mordechai; Kedma, Gabi; Kachlon, Assaf; Elovici, Yuval (November 2014). 'AirHopper: Bridging the Air-Gap between Isolated Networks and Mobile Phones using Radio Frequencies'. arXiv:1411.0237 [cs.CR].
  9. ^ abGuri, Mordechai; Kedma, Gabi; Kachlon, Assaf; Elovici, Yuval (November 2014). 'How to leak sensitive data from an isolated computer (air-gap) to a near by mobile phone - AirHopper'. BGU Cyber Security Labs.
  10. ^Rist, Oliver (2006-05-29). 'Hack Tales: Air-gap networking for the price of a pair of sneakers'. Infoworld. IDG Network. Retrieved 2009-01-16. In high-security situations, various forms of data often must be kept off production networks, due to possible contamination from nonsecure resources — such as, say, the Internet. So IT admins must build enclosed systems to house that data — stand-alone servers, for example, or small networks of servers that aren't connected to anything but one another. There's nothing but air between these and other networks, hence the term air gap, and transferring data between them is done the old-fashioned way: moving disks back and forth by hand, via 'sneakernet'.
  11. ^'Weber vs SEC'(PDF). insurancenewsnet.com. 2012-11-15. p. 35. Archived from the original(PDF) on 2013-12-03. Retrieved 2012-12-06. Stock exchange internal network computer systems are so sensitive that they are “air gapped” and not attached to the internet, in order to protect them from attack, intrusion, or other malicious acts by third party adversaries.
  12. ^'Weber vs SEC'. Industrial internal network computer systems are so sensitive that they are “air gapped” and neither attached to the internet nor insecurely connects to the corporate network, in order to protect them from attack, intrusion, or other malicious acts by third party adversaries.
  13. ^Zetter, Kim (2008-01-04). 'FAA: Boeing's New 787 May Be Vulnerable to Hacker Attack'. Wired Magazine. CondéNet, Inc.Archived from the original on 23 December 2008. Retrieved 2009-01-16. (...Boeing...) wouldn't go into detail about how (...it...) is tackling the issue but says it is employing a combination of solutions that involves some physical separation of the networks, known as air gaps, and software firewalls.
  14. ^Leyden, John (5 Dec 2013). 'Hear that? It's the sound of BadBIOS wannabe chatting over air gaps'. Retrieved 30 December 2014.
  15. ^Guri, Mordechai; Monitz, Matan; Mirski, Yisroel; Elovici, Yuval (April 2015). 'BitWhisper: Covert Signaling Channel between Air-Gapped Computers using Thermal Manipulations'. arXiv:1503.07919 [cs.CR].
  16. ^Guri, Mordechai; Monitz, Matan; Mirski, Yisroel; Elovici, Yuval (March 2015). 'BitWhisper: The Heat is on the Air-Gap'. BGU Cyber Security Labs.
  17. ^Guri, Mordechai; Kachlon, Assaf; Hasson, Ofer; Kedma, Gabi; Mirsky, Yisroel; Elovici, Yuval (August 2015). 'GSMem: Data Exfiltration from Air-Gapped Computers over GSM Frequencies'. 24th USENIX Security Symposium (USENIX Security 15): 849–864. ISBN9781931971232.
  18. ^Guri, Mordechai; Kachlon, Assaf; Hasson, Ofer; Kedma, Gabi; Mirsky, Yisroel; Monitz, Matan; Elovici, Yuval (July 2015). 'GSMem Breaking The Air-Gap'. Cyber Security Labs @ Ben Gurion University.
  19. ^Chris Baraniuk (2016-08-09). ''Project Sauron' malware hidden for five years'. BBC.
  20. ^Cameron Faulkner. 'What is NFC? Everything you need to know'. Techradar.com. Retrieved 30 November 2015.
  21. ^'NFCdrip: NFC Data Exfiltration Research'. Checkmarx. Retrieved 19 December 2018.
  22. ^Carrara, Brent (September 2016). “Air-Gap Covert Channels.” Ph. D. Thesis. University of Ottawa.
  23. ^Carrara, Brent; Adams, Carlisle (2016). 'A Survey and Taxonomy Aimed at the Detection and Measurement of Covert Channels'. Proceedings of the 4th ACM Workshop on Information Hiding and Multimedia Security - IH&MMSec '16. pp. 115–126. doi:10.1145/2909827.2930800. ISBN9781450342902. S2CID34896818.
  24. ^Carrara, Brent; Adams, Carlisle (2016-06-01). 'Out-of-Band Covert Channels—A Survey'. ACM Computing Surveys. 49 (2): 1–36. doi:10.1145/2938370. ISSN0360-0300. S2CID13902799.
  25. ^Cimpanu, Catalin. 'Academics turn RAM into Wi-Fi cards to steal data from air-gapped systems'. ZDNet.

Air Gapping

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