Monday, August 24, 2015

Retrieve gene location info from UCSC hg18/19 using MySQL script

I have a list of gene symbols.

APOB, TTC39B, ATF3, RGS1, LIPG,
I am trying to get the genomic coordinates (as in bp) with +/-5KB position of these genes via UCSC TableBrowser / MySQL server using NCBI 36/hg18 build. I have tried to get this information via TableBrowser, but I can't find the chromStart and chromEnd field in the given table. Am I missing something ?
Also, please share your favorite tutorial / docs that explain the schema/tables in UCSC MySQL server.
Thanks in advance.


 Answer:


from the table browser http://genome.ucsc.edu/cgi-bin/hgTables?command=start , select group= Genes , track= UCSC gene , table=knownGene and then 'describe table schema'
You'll see that knownGene is linked to kgXref :

hg18.kgXref.kgID (via knownGene.name)
and kgXref contains a column named 'geneSymbol'.
all in one, you can get the positions of the transcripts for those genes:

mysql  -h  genome-mysql.cse.ucsc.edu -A -u genome -D hg18 \
-e 'select distinct X.geneSymbol,G.chrom,G.txStart-5000,G.txEnd+5000 \
from knownGene as G, kgXref as X \
where X.geneSymbol in ("APOB", "TTC39B", "ATF3", "RGS1", "LIPG") \
and X.kgId=G.name'
 
+------------+-------+----------------+--------------+
| geneSymbol | chrom | G.txStart-5000 | G.txEnd+5000 |
+------------+-------+----------------+--------------+
| APOB       | chr2  |       21072805 |     21125450 |
| ATF3       | chr1  |      210843616 |    210865739 |
| ATF3       | chr1  |      210800319 |    210865739 |
| ATF3       | chr1  |      210843616 |    210865704 |
| ATF3       | chr1  |      210849982 |    210864212 |
| LIPG       | chr18 |       45337424 |     45378276 |
| LIPG       | chr18 |       45337424 |     45367217 |
| RGS1       | chr1  |      190806479 |    190820782 |
| TTC39B     | chr9  |       15156560 |     15302244 |
| TTC39B     | chr9  |       15156560 |     15227442 |
| TTC39B     | chr9  |       15171584 |     15302244 |
| TTC39B     | chr9  |       15172968 |     15268702 |
| TTC39B     | chr9  |       15172968 |     15227442 |
+------------+-------+----------------+--------------+
I agree that the information is hard to find: I only knew where to find it because I use to play regularly with those tables.
The UCSC mailing list is a good place to find this kind of information. I also did a lot of reverse engineering by just 'greping' the flat files available from the UCSC.
 


 The same script works for hg19 as well.

Friday, August 21, 2015

How to install gcc 4.7 on Ubuntu LTS12?

Question:
I have gcc 4.6 installed on Ubuntu LTS 12.04. How can I upgrade to gcc 4.7?


NOTE!!
You also most likely need to take care of g++-4.7 as well.

So the full commands list will be:

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-4.7 g++-4.7
 
Also, don't forget to update-alternatives, as suggested here

sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.6 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.6 
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.7 40 --slave /usr/bin/g++ g++ /usr/bin/g++-4.7 
sudo update-alternatives --config gcc
 
This is confirmed to work in Ubuntu 12.04

Thursday, August 13, 2015

Testing for SSL-TLS (OWASP-CM-001)

This article is part of the OWASP Testing Guide v3. The entire OWASP Testing Guide v3 can be downloaded here.
OWASP at the moment is working at the OWASP Testing Guide v4: you can browse the Guide here

Brief Summary

Due to historic export restrictions of high grade cryptography, legacy and new web servers are often able and configured to handle weak cryptographic options.
Even if high grade ciphers are normally used and installed, some server misconfiguration could be used to force the use of a weaker cipher to gain access to the supposed secure communication channel.

Testing SSL / TLS Cipher Specifications and Requirements

The http clear-text protocol is normally secured via an SSL or TLS tunnel, resulting in https traffic. In addition to providing encryption of data in transit, https allows the identification of servers (and, optionally, of clients) by means of digital certificates.
Historically, there have been limitations set in place by the U.S. government to allow cryptosystems to be exported only for key sizes of, at most, 40 bits, a key length which could be broken and would allow the decryption of communications. Since then, cryptographic export regulations have been relaxed (though some constraints still hold); however, it is important to check the SSL configuration being used to avoid putting in place cryptographic support which could be easily defeated. SSL-based services should not offer the possibility to choose weak ciphers.
Cipher determination is performed as follows: in the initial phase of a SSL connection setup, the client sends the server a Client Hello message specifying, among other information, the cipher suites that it is able to handle. A client is usually a web browser (most popular SSL client nowadays), but not necessarily, since it can be any SSL-enabled application; the same holds for the server, which needs not be a web server, though this is the most common case. (For example, a noteworthy class of SSL clients is that of SSL proxies such as stunnel (www.stunnel.org) which can be used to allow non-SSL enabled tools to talk to SSL services.) A cipher suite is specified by an encryption protocol (DES, RC4, AES), the encryption key length (such as 40, 56, or 128 bits), and a hash algorithm (SHA, MD5) used for integrity checking. Upon receiving a Client Hello message, the server decides which cipher suite it will use for that session. It is possible (for example, by means of configuration directives) to specify which cipher suites the server will honor. In this way you may control, for example, whether or not conversations with clients will support 40-bit encryption only.

SSL Testing Criteria

Large number of available cipher suites and quick progress in cryptoanalysis makes judging a SSL server a non-trivial task. These criteria are widely recognised as minimum checklist:
  • SSLv2, due to known weaknesses in protocol design [1]
  • SSLv3, due to known weaknesses in protocol design [2]
  • Compression, due to known weaknesses in protocol design [3]
  • Cipher suites with symmetric encryption algorithm smaller than 112 bits
  • X.509 certificates with RSA key smaller than 2048 bits
  • X.509 certificates with DSA key smaller than 2048 bits
  • X.509 certificates signed using MD5 hash, due to known collision attacks on this hash
  • TLS Renegotiation vulnerability [4]
The following standards can be used as reference while assessing SSL servers:
  • NIST SP 800-52 recommends U.S. federal systems to use at least TLS 1.0 with ciphersuites based on RSA or DSA key agreement with ephemeral Diffie-Hellman, 3DES or AES for confidentality and SHA1 for integrity protection. NIST SP 800-52 specifically disallows non-FIPS compliant algorithms like RC4 and MD5. An exception is U.S. federal systems making connections to outside servers, where these algorithms can be used in SSL client mode.
  • PCI-DSS v1.2 in point 4.1 requires compliant parties to use "strong cryptography" without precisely defining key lengths and algorithms. Common interpretation, partially based on previous versions of the standard, is that at least 128 bit key cipher, no export strength algorithms and no SSLv2 should be used[5].
  • SSL Server Rating Guide has been proposed to standardize SSL server assessment and currently is in draft version.
SSL Server Database can be used to assess configuration of publicly available SSL servers[6] based on SSL Rating Guide[7]

Black Box Test and example

In order to detect possible support of weak ciphers, the ports associated to SSL/TLS wrapped services must be identified. These typically include port 443, which is the standard https port; however, this may change because a) https services may be configured to run on non-standard ports, and b) there may be additional SSL/TLS wrapped services related to the web application. In general, a service discovery is required to identify such ports.
The nmap scanner, via the “–sV” scan option, is able to identify SSL services. Vulnerability Scanners, in addition to performing service discovery, may include checks against weak ciphers (for example, the Nessus scanner has the capability of checking SSL services on arbitrary ports, and will report weak ciphers).

Example 1. SSL service recognition via nmap.
[root@test]# nmap -F -sV localhost

Starting nmap 3.75 ( http://www.insecure.org/nmap/ ) at 2005-07-27 14:41 CEST
Interesting ports on localhost.localdomain (127.0.0.1):
(The 1205 ports scanned but not shown below are in state: closed)

PORT      STATE SERVICE         VERSION
443/tcp   open  ssl             OpenSSL
901/tcp   open  http            Samba SWAT administration server
8080/tcp  open  http            Apache httpd 2.0.54 ((Unix) mod_ssl/2.0.54 OpenSSL/0.9.7g PHP/4.3.11)
8081/tcp  open  http            Apache Tomcat/Coyote JSP engine 1.0

Nmap run completed -- 1 IP address (1 host up) scanned in 27.881 seconds
[root@test]# 

Example 2. Identifying weak ciphers with Nessus. The following is an anonymized excerpt of a report generated by the Nessus scanner, corresponding to the identification of a server certificate allowing weak ciphers (see underlined text).
 https (443/tcp)
 Description
 Here is the SSLv2 server certificate:
 Certificate:
 Data:
 Version: 3 (0x2)
 Serial Number: 1 (0x1)
 Signature Algorithm: md5WithRSAEncryption
 Issuer: C=**, ST=******, L=******, O=******, OU=******, CN=******
 Validity
 Not Before: Oct 17 07:12:16 2002 GMT
 Not After : Oct 16 07:12:16 2004 GMT
 Subject: C=**, ST=******, L=******, O=******, CN=******
 Subject Public Key Info:
 Public Key Algorithm: rsaEncryption
 RSA Public Key: (1024 bit)
 Modulus (1024 bit):
 00:98:4f:24:16:cb:0f:74:e8:9c:55:ce:62:14:4e:
 6b:84:c5:81:43:59:c1:2e:ac:ba:af:92:51:f3:0b:
 ad:e1:4b:22:ba:5a:9a:1e:0f:0b:fb:3d:5d:e6:fc:
 ef:b8:8c:dc:78:28:97:8b:f0:1f:17:9f:69:3f:0e:
 72:51:24:1b:9c:3d:85:52:1d:df:da:5a:b8:2e:d2:
 09:00:76:24:43:bc:08:67:6b:dd:6b:e9:d2:f5:67:
 e1:90:2a:b4:3b:b4:3c:b3:71:4e:88:08:74:b9:a8:
 2d:c4:8c:65:93:08:e6:2f:fd:e0:fa:dc:6d:d7:a2:
 3d:0a:75:26:cf:dc:47:74:29
 Exponent: 65537 (0x10001)
 X509v3 extensions:
 X509v3 Basic Constraints:
 CA:FALSE
 Netscape Comment:
 OpenSSL Generated Certificate
 Page 10
 Network Vulnerability Assessment Report 25.05.2005
 X509v3 Subject Key Identifier:
 10:00:38:4C:45:F0:7C:E4:C6:A7:A4:E2:C9:F0:E4:2B:A8:F9:63:A8
 X509v3 Authority Key Identifier:
 keyid:CE:E5:F9:41:7B:D9:0E:5E:5D:DF:5E:B9:F3:E6:4A:12:19:02:76:CE
 DirName:/C=**/ST=******/L=******/O=******/OU=******/CN=******
 serial:00
 Signature Algorithm: md5WithRSAEncryption
 7b:14:bd:c7:3c:0c:01:8d:69:91:95:46:5c:e6:1e:25:9b:aa:
 8b:f5:0d:de:e3:2e:82:1e:68:be:97:3b:39:4a:83:ae:fd:15:
 2e:50:c8:a7:16:6e:c9:4e:76:cc:fd:69:ae:4f:12:b8:e7:01:
 b6:58:7e:39:d1:fa:8d:49:bd:ff:6b:a8:dd:ae:83:ed:bc:b2:
 40:e3:a5:e0:fd:ae:3f:57:4d:ec:f3:21:34:b1:84:97:06:6f:
 f4:7d:f4:1c:84:cc:bb:1c:1c:e7:7a:7d:2d:e9:49:60:93:12:
 0d:9f:05:8c:8e:f9:cf:e8:9f:fc:15:c0:6e:e2:fe:e5:07:81:
 82:fc
 Here is the list of available SSLv2 ciphers:
 RC4-MD5
 EXP-RC4-MD5
 RC2-CBC-MD5
 EXP-RC2-CBC-MD5
 DES-CBC-MD5
 DES-CBC3-MD5
 RC4-64-MD5
 The SSLv2 server offers 5 strong ciphers, but also 0 medium strength and 2 weak "export class" ciphers.
 The weak/medium ciphers may be chosen by an export-grade or badly configured client software. They only offer a limited protection against a brute force attack
 Solution: disable those ciphers and upgrade your client software if necessary.
 See http://support.microsoft.com/default.aspx?scid=kben-us216482
 or http://httpd.apache.org/docs-2.0/mod/mod_ssl.html#sslciphersuite
 This SSLv2 server also accepts SSLv3 connections.
 This SSLv2 server also accepts TLSv1 connections.
 
 Vulnerable hosts
 (list of vulnerable hosts follows)

Example 3. Manually audit weak SSL cipher levels with OpenSSL. The following will attempt to connect to Google.com with SSLv2.
[root@test]# openssl s_client -no_tls1 -no_ssl3 -connect www.google.com:443
CONNECTED(00000003)
depth=0 /C=US/ST=California/L=Mountain View/O=Google Inc/CN=www.google.com
verify error:num=20:unable to get local issuer certificate
verify return:1
depth=0 /C=US/ST=California/L=Mountain View/O=Google Inc/CN=www.google.com
verify error:num=27:certificate not trusted
verify return:1
depth=0 /C=US/ST=California/L=Mountain View/O=Google Inc/CN=www.google.com
verify error:num=21:unable to verify the first certificate
verify return:1
---
Server certificate
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----
subject=/C=US/ST=California/L=Mountain View/O=Google Inc/CN=www.google.com
issuer=/C=ZA/ST=Western Cape/L=Cape Town/O=Thawte Consulting cc/OU=Certification Services Division/CN=Thawte Premium Server CA/emailAddress=premium-server@thawte.com
---
No client certificate CA names sent
---
Ciphers common between both SSL endpoints:
RC4-MD5         EXP-RC4-MD5     RC2-CBC-MD5
EXP-RC2-CBC-MD5 DES-CBC-MD5     DES-CBC3-MD5
RC4-64-MD5
---
SSL handshake has read 1023 bytes and written 333 bytes
---
New, SSLv2, Cipher is DES-CBC3-MD5
Server public key is 1024 bit
Compression: NONE
Expansion: NONE
SSL-Session:
    Protocol  : SSLv2
    Cipher    : DES-CBC3-MD5
    Session-ID: 709F48E4D567C70A2E49886E4C697CDE
    Session-ID-ctx:
    Master-Key: 649E68F8CF936E69642286AC40A80F433602E3C36FD288C3
    Key-Arg   : E8CB6FEB9ECF3033
    Start Time: 1156977226
    Timeout   : 300 (sec)
    Verify return code: 21 (unable to verify the first certificate)
---
closed

Example 4. Testing supported protocols and ciphers using SSLScan.
SSLScan is a free command line tool that scans a HTTPS service to enumerate what protocols (supports SSLv2, SSLv3 and TLS1) and what ciphers the HTTPS service supports. It runs both on Linux and Windows OS (OSX not tested) and is released under a open source license.
[user@test]$ ./SSLScan --no-failed mail.google.com
                   _
           ___ ___| |___  ___ __ _ _ __
          / __/ __| / __|/ __/ _` | '_ \
          \__ \__ \ \__ \ (_| (_| | | | |
          |___/___/_|___/\___\__,_|_| |_|

                  Version 1.9.0-win
             http://www.titania.co.uk
 Copyright 2010 Ian Ventura-Whiting / Michael Boman
    Compiled against OpenSSL 0.9.8n 24 Mar 2010

Testing SSL server mail.google.com on port 443

  Supported Server Cipher(s):
    accepted  SSLv3  256 bits  AES256-SHA
    accepted  SSLv3  128 bits  AES128-SHA
    accepted  SSLv3  168 bits  DES-CBC3-SHA
    accepted  SSLv3  128 bits  RC4-SHA
    accepted  SSLv3  128 bits  RC4-MD5
    accepted  TLSv1  256 bits  AES256-SHA
    accepted  TLSv1  128 bits  AES128-SHA
    accepted  TLSv1  168 bits  DES-CBC3-SHA
    accepted  TLSv1  128 bits  RC4-SHA
    accepted  TLSv1  128 bits  RC4-MD5

  Prefered Server Cipher(s):
    SSLv3  128 bits  RC4-SHA
    TLSv1  128 bits  RC4-SHA

  SSL Certificate:
    Version: 2
    Serial Number: -4294967295
    Signature Algorithm: sha1WithRSAEncryption
    Issuer: /C=ZA/O=Thawte Consulting (Pty) Ltd./CN=Thawte SGC CA
    Not valid before: Dec 18 00:00:00 2009 GMT
    Not valid after: Dec 18 23:59:59 2011 GMT
    Subject: /C=US/ST=California/L=Mountain View/O=Google Inc/CN=mail.google.com
    Public Key Algorithm: rsaEncryption
    RSA Public Key: (1024 bit)
      Modulus (1024 bit):
          00:d9:27:c8:11:f2:7b:e4:45:c9:46:b6:63:75:83:
          b1:77:7e:17:41:89:80:38:f1:45:27:a0:3c:d9:e8:
          a8:00:4b:d9:07:d0:ba:de:ed:f4:2c:a6:ac:dc:27:
          13:ec:0c:c1:a6:99:17:42:e6:8d:27:d2:81:14:b0:
          4b:82:fa:b2:c5:d0:bb:20:59:62:28:a3:96:b5:61:
          f6:76:c1:6d:46:d2:fd:ba:c6:0f:3d:d1:c9:77:9a:
          58:33:f6:06:76:32:ad:51:5f:29:5f:6e:f8:12:8b:
          ad:e6:c5:08:39:b3:43:43:a9:5b:91:1d:d7:e3:cf:
          51:df:75:59:8e:8d:80:ab:53
      Exponent: 65537 (0x10001)
    X509v3 Extensions:
      X509v3 Basic Constraints: critical
        CA:FALSE      X509v3 CRL Distribution Points: 
        URI:http://crl.thawte.com/ThawteSGCCA.crl
      X509v3 Extended Key Usage: 
        TLS Web Server Authentication, TLS Web Client Authentication, Netscape Server Gated Crypto      Authority Information Access: 
        OCSP - URI:http://ocsp.thawte.com
        CA Issuers - URI:http://www.thawte.com/repository/Thawte_SGC_CA.crt
  Verify Certificate:
    unable to get local issuer certificate


Renegotiation requests supported

Example 5. Testing common SSL flaws with ssl_tests
ssl_tests (http://www.pentesterscripting.com/discovery/ssl_tests) is a bash script that uses sslscan and openssl to check for various flaws - ssl version 2, weak ciphers, md5withRSAEncryption,SSLv3 Force Ciphering Bug/Renegotiation.

[user@test]$ ./ssl_test.sh 192.168.1.3 443
+++++++++++++++++++++++++++++++++++++++++++++++++
SSL Tests - v2, weak ciphers, MD5, Renegotiation
by Aung Khant, http://yehg.net
+++++++++++++++++++++++++++++++++++++++++++++++++

[*] testing on 192.168.1.3:443 ..

[*] tesing for sslv2 ..
[*] sslscan 192.168.1.3:443 | grep Accepted  SSLv2
    Accepted  SSLv2  168 bits  DES-CBC3-MD5
    Accepted  SSLv2  56 bits   DES-CBC-MD5
    Accepted  SSLv2  40 bits   EXP-RC2-CBC-MD5
    Accepted  SSLv2  128 bits  RC2-CBC-MD5
    Accepted  SSLv2  40 bits   EXP-RC4-MD5
    Accepted  SSLv2  128 bits  RC4-MD5


[*] testing for weak ciphers ...
[*] sslscan 192.168.1.3:443 | grep  40 bits | grep Accepted
    Accepted  SSLv2  40 bits   EXP-RC2-CBC-MD5
    Accepted  SSLv2  40 bits   EXP-RC4-MD5
    Accepted  SSLv3  40 bits   EXP-EDH-RSA-DES-CBC-SHA
    Accepted  SSLv3  40 bits   EXP-DES-CBC-SHA
    Accepted  SSLv3  40 bits   EXP-RC2-CBC-MD5
    Accepted  SSLv3  40 bits   EXP-RC4-MD5
    Accepted  TLSv1  40 bits   EXP-EDH-RSA-DES-CBC-SHA
    Accepted  TLSv1  40 bits   EXP-DES-CBC-SHA
    Accepted  TLSv1  40 bits   EXP-RC2-CBC-MD5
    Accepted  TLSv1  40 bits   EXP-RC4-MD5

[*] sslscan 192.168.1.3:443 | grep  56 bits | grep Accepted
    Accepted  SSLv2  56 bits   DES-CBC-MD5
    Accepted  SSLv3  56 bits   EDH-RSA-DES-CBC-SHA
    Accepted  SSLv3  56 bits   DES-CBC-SHA
    Accepted  TLSv1  56 bits   EDH-RSA-DES-CBC-SHA
    Accepted  TLSv1  56 bits   DES-CBC-SHA


[*] testing for MD5 certificate ..
[*] sslscan 192.168.1.3:443 | grep MD5WithRSAEncryption

[*] testing for SSLv3 Force Ciphering Bug/Renegotiation ..
[*] echo R | openssl s_client -connect 192.168.1.3:443 | grep DONE
depth=0 /C=DE/ST=Berlin/L=Berlin/O=XAMPP/OU=XAMPP/CN=localhost/emailAddress=admin@localhost
verify error:num=18:self signed certificate
verify return:1
depth=0 /C=DE/ST=Berlin/L=Berlin/O=XAMPP/OU=XAMPP/CN=localhost/emailAddress=admin@localhost
verify return:1
RENEGOTIATING
depth=0 /C=DE/ST=Berlin/L=Berlin/O=XAMPP/OU=XAMPP/CN=localhost/emailAddress=admin@localhost
verify error:num=18:self signed certificate
verify return:1
depth=0 /C=DE/ST=Berlin/L=Berlin/O=XAMPP/OU=XAMPP/CN=localhost/emailAddress=admin@localhost
verify return:1
DONE


[*] done

White Box Test and example

Check the configuration of the web servers which provide https services. If the web application provides other SSL/TLS wrapped services, these should be checked as well.
Example: The following registry path in Microsoft Windows 2003 defines the ciphers available to the server:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\SCHANNEL\Ciphers\

Testing SSL certificate validity – client and server

When accessing a web application via the https protocol, a secure channel is established between the client (usually the browser) and the server. The identity of one (the server) or both parties (client and server) is then established by means of digital certificates. In order for the communication to be set up, a number of checks on the certificates must be passed. While discussing SSL and certificate based authentication is beyond the scope of this Guide, we will focus on the main criteria involved in ascertaining certificate validity: a) checking if the Certificate Authority (CA) is a known one (meaning one considered trusted), b) checking that the certificate is currently valid, and c) checking that the name of the site and the name reported in the certificate match. Remember to upgrade your browser because CA certs expired too, in every release of the browser, CA Certs has been renewed. Moreover it's important to update the browser because more web sites require strong cipher more of 40 or 56 bit.
Let’s examine each check more in detail.
a) Each browser comes with a preloaded list of trusted CAs, against which the certificate signing CA is compared (this list can be customized and expanded at will). During the initial negotiations with an https server, if the server certificate relates to a CA unknown to the browser, a warning is usually raised. This happens most often because a web application relies on a certificate signed by a self-established CA. Whether this is to be considered a concern depends on several factors. For example, this may be fine for an Intranet environment (think of corporate web email being provided via https; here, obviously all users recognize the internal CA as a trusted CA). When a service is provided to the general public via the Internet, however (i.e. when it is important to positively verify the identity of the server we are talking to), it is usually imperative to rely on a trusted CA, one which is recognized by all the user base (and here we stop with our considerations; we won’t delve deeper in the implications of the trust model being used by digital certificates).
b) Certificates have an associated period of validity, therefore they may expire. Again, we are warned by the browser about this. A public service needs a temporally valid certificate; otherwise, it means we are talking with a server whose certificate was issued by someone we trust, but has expired without being renewed.
c) What if the name on the certificate and the name of the server do not match? If this happens, it might sound suspicious. For a number of reasons, this is not so rare to see. A system may host a number of name-based virtual hosts, which share the same IP address and are identified by means of the HTTP 1.1 Host: header information. In this case, since the SSL handshake checks the server certificate before the HTTP request is processed, it is not possible to assign different certificates to each virtual server. Therefore, if the name of the site and the name reported in the certificate do not match, we have a condition which is typically signalled by the browser. To avoid this, one of two techniques should be used. First is Server Name Indication (SNI), which is a TLS extension from RFC 3546; and second is IP-based virtual servers must be used. [2] and [3] describe techniques to deal with this problem and allow name-based virtual hosts to be correctly referenced.

Black Box Testing and examples

Examine the validity of the certificates used by the application. Browsers will issue a warning when encountering expired certificates, certificates issued by untrusted CAs, and certificates which do not match namewise with the site to which they should refer. By clicking on the padlock which appears in the browser window when visiting an https site, you can look at information related to the certificate – including the issuer, period of validity, encryption characteristics, etc.
If the application requires a client certificate, you probably have installed one to access it. Certificate information is available in the browser by inspecting the relevant certificate(s) in the list of the installed certificates.
These checks must be applied to all visible SSL-wrapped communication channels used by the application. Though this is the usual https service running on port 443, there may be additional services involved depending on the web application architecture and on deployment issues (an https administrative port left open, https services on non-standard ports, etc.). Therefore, apply these checks to all SSL-wrapped ports which have been discovered. For example, the nmap scanner features a scanning mode (enabled by the –sV command line switch) which identifies SSL-wrapped services. The Nessus vulnerability scanner has the capability of performing SSL checks on all SSL/TLS-wrapped services.
Examples
Rather than providing a fictitious example, we have inserted an anonymized real-life example to stress how frequently one stumbles on https sites whose certificates are inaccurate with respect to naming.
The following screenshots refer to a regional site of a high-profile IT company.
Warning issued by Microsoft Internet Explorer. We are visiting an .it site and the certificate was issued to a .com site! Internet Explorer warns that the name on the certificate does not match the name of the site.

SSL Certificate Validity Testing IE Warning.gif

Warning issued by Mozilla Firefox. The message issued by Firefox is different – Firefox complains because it cannot ascertain the identity of the .com site the certificate refers to because it does not know the CA which signed the certificate. In fact, Internet Explorer and Firefox do not come preloaded with the same list of CAs. Therefore, the behavior experienced with various browsers may differ.

SSL Certificate Validity Testing Firefox Warning.gif

White Box Testing and examples

Examine the validity of the certificates used by the application at both server and client levels. The usage of certificates is primarily at the web server level; however, there may be additional communication paths protected by SSL (for example, towards the DBMS). You should check the application architecture to identify all SSL protected channels.

References

Whitepapers
Tools
  • Vulnerability scanners may include checks regarding certificate validity, including name mismatch and time expiration. They usually report other information as well, such as the CA which issued the certificate. Remember that there is no unified notion of a “trusted CA”; what is trusted depends on the configuration of the software and on the human assumptions made beforehand. Browsers come with a preloaded list of trusted CAs. If your web application relies on a CA which is not in this list (for example, because you rely on a self-made CA), you should take into account the process of configuring user browsers to recognize the CA.
  • The Nessus scanner includes a plugin to check for expired certificates or certificates which are going to expire within 60 days (plugin “SSL certificate expiry”, plugin id 15901). This plugin will check certificates installed on the server.
  • Vulnerability scanners may include checks against weak ciphers. For example, the Nessus scanner (http://www.nessus.org) has this capability and flags the presence of SSL weak ciphers (see example provided above).
  • You may also rely on specialized tools such as SSL Digger (http://www.mcafee.com/us/downloads/free-tools/ssldigger.aspx), or – for the command line oriented – experiment with the openssl tool, which provides access to OpenSSL cryptographic functions directly from a Unix shell (may be already available on *nix boxes, otherwise see www.openssl.org).
  • To identify SSL-based services, use a vulnerability scanner or a port scanner with service recognition capabilities. The nmap scanner features a “-sV” scanning option which tries to identify services, while the nessus vulnerability scanner has the capability of identifying SSL-based services on arbitrary ports and to run vulnerability checks on them regardless of whether they are configured on standard or non-standard ports.
  • In case you need to talk to a SSL service but your favourite tool doesn’t support SSL, you may benefit from a SSL proxy such as stunnel; stunnel will take care of tunneling the underlying protocol (usually http, but not necessarily so) and communicate with the SSL service you need to reach.
  • Finally, a word of advice. Though it may be tempting to use a regular browser to check certificates, there are various reasons for not doing so. Browsers have been plagued by various bugs in this area, and the way the browser will perform the check might be influenced by configuration settings that may not be evident. Instead, rely on vulnerability scanners or on specialized tools to do the job.

Rip SSLv3

The Internet community officially banishes the notoriously unsafe Secure Sockets Layer protocol.
The venerable “secure” network protocol Secure Sockets Layer (SSL) v3 has met its end. SSL has co-existed on the Internet alongside its presumed successor TLS for many years, even though experts have long warned of its shortcomings. A recent rash of high-profile incidents, however, including the famous POODLE exploit, have finally caused the Internet Engineering Task Force (IETF) to take action. Request for Comment (RFC) 7568 “Deprecating Secure Sockets Layer Version 3.0” officially states the requirement that SSLv3 should not be supported.
The RFC is unusually blunt, with its all-cap stipulation that “SSLv3 MUST NOT be used.” Although most systems today support the safer TLS, many provide fallback support for SSLv3 if an SSL connection is requested. Attackers have perfected the technique of requesting an SSL connection then use one of the many exploits associated with SSL. RFC 7568 states that “Any party receiving a Hello message with the version set to {3,00} MUST respond with a ‘protocol_version’ alert message and close the connection.”
Many OS and application vendors have already turned off support for SSLv3 through patches and security updates. 

How to enable TLS 1.2 on Windows Server 2008 R2

Problem

How to enable TLS 1.2 on Windows Server 2008 R2?

Resolution

QuoVadis recommends enabling and using the TLS 1.2 protocol on your server.  TLS 1.2 has improvements over previous versions of the TLS and SSL protocol which will improve your level of security.  By default, Windows Server 2008 R2 does not have this feature enabled.  This KB article will describe the process to enable this.
  1. Start the registry editor by clicking on Start and Run. Type in "regedit" into the Run field (without quotations).

  2. Highlight Computer at the top of the registry tree.  Backup the registry first by clicking on File and then onExport.  Select a file location to save the registry file.

  3. Note: You will be editing the registry.  This could have detrimental effects on your computer if done incorrectly, so it is strongly advised to make a backup.

  4. Browse to the following registry key:
    HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\SCHANNEL\Protocols

  5. Right click on the Protocols folder and select New and then Key from the drop-down menu. This will create new folder.  Rename this folder to TLS 1.2.

  6. Right click on the TLS 1.2 key and add two new keys underneath it.

  7. Rename the two new keys as:
    • Client
    • Server

  8. Right click on the Client key and select New and then DWORD (32-bit) Value from the drop-down list.

  9. Rename the DWORD to DisabledByDefault.

  10. Right-click the name DisabledByDefault and select Modify... from the drop-down menu.

  11. Ensure that the Value data field is set to 0 and the Base is Hexadecimal.  Click on OK.

  12. Create another DWORD for the Client key as you did in Step 7.

  13. Rename this second DWORD to Enabled.

  14. Right-click the name Enabled and select Modify... from the drop-down menu.

  15. Ensure that the Value data field is set to 1 and the Base is Hexadecimal. Click on OK.

  16. Repeat steps 7 to 14 for the Server key (by creating two DWORDs, DisabledByDefault and Enabled, and their values underneath the Server key).

  17. Reboot the server.
Your server should now support TLS 1.2.

Note: This article cannot be used on a Windows Server 2003 (IIS 6).  Windows Server 2003 does not support the TLS 1.2 protocol.

Resolution for POODLE SSLv3.0 vulnerability (CVE-2014-3566) in httpd: Migrate to TLS

 Issue

  • How do I avoid impact to httpd from CVE-2014-3566?

Environment

  • Red Hat Enterprise Linux 5, 6, 7
  • Red Hat JBoss Enterprise Application Platform (EAP) 5, 6
  • JBoss Enterprise Web Server (EWS) 1, 2
  • Inktank Ceph Enterprise (ICE) 1
  • Red Hat Storage Console
  • Red Hat Enterprise Virtualization

Resolution

To avoid this vulnerability, Red Hat recommends disabling SSL and using only TLSv1.1 or TLSv1.2. Backwards compatibility can be achieved using TLSv1.0. Many products Red Hat supports have the ability to use SSLv2 or SSLv3 protocols, or enable them by default. However use of SSLv2 or SSLv3 is now strongly recommended against.
The SSL/TLS support in httpd can be provided by the mod_ssl module using the OpenSSL library, or by the mod_nss module using the NSS library.
Examples below enable all TLS versions currently supported by specified product versions.

Disabling SSL 3.0 in mod_ssl

To mitigate this vulnerability as it affects httpd using mod_ssl, set the SSLProtocol directive as follows in/etc/httpd/conf.d/ssl.conf:
Note: This directive must either be located at the topmost level of the configuration file, or inside the default virtual host configuration for an address.
Option 1: Disable SSLv2 and SSLv3 (Enable everything except SSLv2 and SSLv3)
    SSLProtocol All -SSLv2 -SSLv3
Then restart httpd:
    # service httpd restart
Option 2: Disable everything except TLSv1.x
On Red Hat Enterprise Linux 7 or Red Hat Enterprise Linux 6.6 and later:
    SSLProtocol -All +TLSv1 +TLSv1.1 +TLSv1.2
On other platforms, including Red Hat Enterprise Linux 5
    SSLProtocol -All +TLSv1
Then restart httpd:
    # service httpd restart

Disabling SSL 3.0 in mod_nss

To mitigate this vulnerability as it affects httpd using mod_nss, set the NSSProtocol directive as follows in/etc/httpd/conf.d/nss.conf:
Red Hat Enterprise Linux 6 and later:
  NSSProtocol TLSv1.0,TLSv1.1
Red Hat Enterprise Linux 5:
  NSSProtocol TLSv1.0
Then restart httpd:
    # service httpd restart

Root Cause

A vulnerability was found in the SSLv3.0 protocol. This vulnerability allows a man-in-the-middle attacker to decrypt ciphertext using a padding oracle side-channel attack. For more information about this vulnerability, refer to the following article: POODLE: SSLv3.0 vulnerability (CVE-2014-3566)

Diagnostic Steps

For diagnostic steps, refer to the following article: POODLE: SSLv3.0 vulnerability (CVE-2014-3566)