精华内容
下载资源
问答
  • blat

    2019-10-21 16:20:45
    Blat 是一个命令行发邮件的小工具,仅支持简单的SMTP协议,需要SMTP服务器的支持。 据说现在新申请的邮箱已经不支持SMTP服务了,是为了抑制垃圾邮件而采取的措施。 但是,Blat也是一个非常方便的小工具,基本上可以...

    Blat 是一个命令行发邮件的小工具,仅支持简单的SMTP协议,需要SMTP服务器的支持。
    据说现在新申请的邮箱已经不支持SMTP服务了,是为了抑制垃圾邮件而采取的措施。
    但是,Blat也是一个非常方便的小工具,基本上可以满足一般人的需求。

     

    简单使用方法:

    在控制台中切换到Blat.exe V2.6.2文件所在地址(仅需Blat.exe文件);

    配置Blat的SMTP服务器:
    blat -install sever usr try port [profile]
    163邮箱举例:
    blat -install smtp.163.com user@163.com 3 25
    其中的smtp.163.com是163的smtp服务器地址;user@163.com是自己的邮箱名,3是指尝试发送的次数,25是端口号;
    [profile]指的是这个配置文件的名称,可以不填,也可以自己用一个名字,等到发送邮件的时候,就可以使用-p选项来指定配置,如果同时使用多个邮箱的话,这个就很方便了。
     

    发送邮件:
    blat C:/mail.txt -to demo@demo.com -attach "C:/fujia.txt" -s "zhuti" -u user@163.com -pw password -charset Gb2312
    其中的mail是写好的邮件文件(邮件正文,已文件方式保存),-to demo@demo.com是收件人的地址,-attach "C:/fujia.txt"是附件地址,-s "zhuti"主题,-u user@163.com登陆服务器的用户名,-pw password密码, -charset Gb2312是中文编码

    显示信息:
    Blat v2.6.2 w/GSS encryption (build : Feb 25 2007 12:06:19)
    Sending C:/mail.txt to demo@demo.com
    Subject: zhuti
    Login name is user@163.com
    Attached binary file: C:/fujia.txt
    如果只是以上信息,而没有错误提示,那么邮件就发送成功了。
     

    附:

    Blat v2.6.2 w/GSS encryption (build : Feb 25 2007 12:06:19)

    Win32 console utility to send mail via SMTP or post to usenet via NNTP
    by P.Mendes,M.Neal,G.Vollant,T.Charron,T.Musson,H.Pesonen,A.Donchey,C.Hyde
    http://www.blat.net
    syntax:
    Blat <filename> -to <recipient> [optional switches (see below)]
    Blat -install <server addr> <sender's addr> [<try>[<port>[<profile>]]] [-q]
    Blat -profile [-delete | "<default>"] [profile1] [profileN] [-q]
    Blat -h

    -------------------------------- Installation ---------------------------------
    -install[SMTP|NNTP|POP3|IMAP] <server addr> <sender email addr> [<try n times>
                    [<port> [<profile> [<username> [<password>]]]]]
                    : set server, sender, number of tries and port for profile
                      (<try n times> and <port> may be replaced by '-')
                      port defaults are SMTP=25, NNTP=119, POP3=110, IMAP=143
                      default profile can be specified with a '-'
                      username and/or password may be stored to the registry
                      order of options is specific
                      use -installNNTP for storing NNTP information
                      use -installPOP3 for storing POP3 information
                          (sender and try are ignored, use '-' in place of these)
                      use -installIMAP for storing IMAP information
                          (sender and try are ignored, use '-' in place of these)

    --------------------------------- The Basics ----------------------------------
    <filename>      : file with the message body to be sent
                      if your message body is on the command line, use a hyphen (-)
                      as your first argument, and -body followed by your message
                      if your message will come from the console/keyboard, use the
                      hyphen as your first argument, but do not use -body option.
    -of <file>      : text file containing more options (also -optionfile)
    -to <recipient> : recipient list (also -t) (comma separated)
    -tf <file>      : recipient list filename
    -cc <recipient> : carbon copy recipient list (also -c) (comma separated)
    -cf <file>      : cc recipient list filename
    -bcc <recipient>: blind carbon copy recipient list (also -b)
                      (comma separated)
    -bf <file>      : bcc recipient list filename
    -maxNames <x>   : send to groups of <x> number of recipients
    -ur             : set To: header to Undisclosed Recipients if not using the
                      -to and -cc options
    -subject <subj> : subject line, surround with quotes to include spaces(also -s)
    -ss             : suppress subject line if not defined
    -sf <file>      : file containing subject line
    -body <text>    : message body, surround with quotes to include spaces
    -sig <file>     : text file containing your email signature
    -tag <file>     : text file containing taglines, to be randomly chosen
    -ps <file>      : final message text, possibly for unsubscribe instructions

    ----------------------------- Registry overrides ------------------------------
    -p <profile>    : send with server, user, and port defined in <profile>
                    : use username and password if defined in <profile>
    -profile        : list all profiles in the Registry
    -server <addr> : specify SMTP server to be used (optionally, addr:port)
    -serverSMTP <addr>
                    : same as -server
    -serverNNTP <addr>
                    : specify NNTP server to be used (optionally, addr:port)
    -serverPOP3 <addr>
                    : specify POP3 server to be used (optionally, addr:port)
                      when POP3 access is required before sending email
    -serverIMAP <addr>
                    : specify IMAP server to be used (optionally, addr:port)
                      when IMAP access is required before sending email
    -f <sender>     : override the default sender address (must be known to server)
    -i <addr>       : a 'From:' address, not necessarily known to the server
    -port <port>    : port to be used on the SMTP server, defaults to SMTP (25)
    -portSMTP <port>: same as -port
    -portNNTP <port>: port to be used on the NNTP server, defaults to NNTP (119)
    -portPOP3 <port>: port to be used on the POP3 server, defaults to POP3 (110)
    -portIMAP <port>: port to be used on the IMAP server, defaults to IMAP (110)
    -u <username>   : username for AUTH LOGIN (use with -pw)
    -pw <password> : password for AUTH LOGIN (use with -u)
    -pu <username> : username for POP3 LOGIN (use with -ppw)
    -ppw <password> : password for POP3 LOGIN (use with -pu)
    -iu <username> : username for IMAP LOGIN (use with -ppw)
    -ipw <password> : password for IMAP LOGIN (use with -pu)

    ---------------------- Miscellaneous RFC header switches ----------------------
    -organization <organization>
                    : Organization field (also -o and -org)
    -ua             : include User-Agent header line instead of X-Mailer
    -x <X-Header: detail>
                    : custom 'X-' header. eg: -x "X-INFO: Blat is Great!"
    -noh            : prevent X-Mailer/User-Agent header from showing Blat homepage
    -noh2           : prevent X-Mailer header entirely
    -d              : request disposition notification
    -r              : request return receipt
    -charset <cs>   : user defined charset. The default is ISO-8859-1
    -a1 <header>    : add custom header line at the end of the regular headers
    -a2 <header>    : same as -a1, for a second custom header line
    -dsn <nsfd>     : use Delivery Status Notifications (RFC 3461)
                      n = never, s = successful, f = failure, d = delayed
                      can be used together, however N takes precedence
    -hdrencb        : use base64 for encoding headers, if necessary
    -hdrencq        : use quoted-printable for encoding headers, if necessary
    -priority <pr> : set message priority 0 for low, 1 for high
    -sensitivity <s>   : set message sensitity 0 for personal, 1 for private,
                      2 for company-confidential

    ----------------------- Attachment and encoding options -----------------------
    -attach <file> : attach binary file(s) to message (filenames comma separated)
    -attacht <file> : attach text file(s) to message (filenames comma separated)
    -attachi <file> : attach text file(s) as INLINE (filenames comma separated)
    -embed <file>   : embed file(s) in HTML. Object tag in HTML must specify
                      content-id using cid: tag. eg: <img src="cid:image.jpg">
    -af <file>      : file containing list of binary file(s) to attach (comma
                      separated)
    -atf <file>     : file containing list of text file(s) to attach (comma
                      separated)
    -aef <file>     : file containing list of embed file(s) to attach (comma
                      separated)
    -base64         : send binary files using base64 (binary MIME)
    -uuencode       : send binary files UUEncoded
    -enriched       : send an enriched text message (Content-Type=text/enriched)
    -unicode        : message body is in 16- or 32-bit Unicode format
    -html           : send an HTML message (Content-Type=text/html)
    -alttext <text> : plain text for use as alternate text
    -alttextf <file>: plain text file for use as alternate text
    -mime           : MIME Quoted-Printable Content-Transfer-Encoding
    -8bitmime       : ask for 8bit data support when sending MIME
    -multipart <size>
                    : send multipart messages, breaking attachments on <size>
                      KB boundaries, where <size> is per 1000 bytes
    -nomps                : do not allow multipart messages

    ---------------------------- NNTP specific options ----------------------------
    -groups <usenet groups>
                    : list of newsgroups (comma separated)

    -------------------------------- Other options --------------------------------
    -xtndxmit       : Attempt to use POP3 to transmit when accessing POP3 first
    -h              : displays this help (also -?, /?, -help or /help)
    -q              : suppresses all output to the screen
    -debug          : echoes server communications to a log file or screen
                      (overrides -q if echoes to the screen)
    -log <file>     : log everything but usage to <file>
    -timestamp      : when -log is used, a timestamp is added to each log line
    -ti <n>         : set timeout to 'n' seconds. Blat will wait 'n' seconds for
                      server responses
    -try <n times> : how many times blat should try to send (1 to 'INFINITE')
    -binary         : do not convert ASCII | (pipe, 0x7c) to CrLf in the message
                      body
    -hostname <hst> : select the hostname used to send the message via SMTP
                      this is typically your local machine name
    -raw            : do not add CR/LF after headers
    -delay <x>      : wait x seconds between messages being sent when used with
                      -maxnames or -multipart
    -comment <char> : use this character to mark the start of commments in
                      options files and recipient list files. The default is ;
    -superdebug     : hex/ascii dump the data between Blat and the server
    -superdebugT    : ascii dump the data between Blat and the server
    -------------------------------------------------------------------------------

    Note that if the '-i' option is used, <sender> is included in 'Reply-to:'
    and 'Sender:' fields in the header of the message.

    Optionally, the following options can be used instead of the -f and -i
    options:

    -mailfrom <addr>   The RFC 821 MAIL From: statement
    -from <addr>       The RFC 822 From: statement
    -replyto <addr>    The RFC 822 Reply-To: statement
    -returnpath <addr> The RFC 822 Return-Path: statement
    -sender <addr>     The RFC 822 Sender: statement

    For backward consistency, the -f and -i options have precedence over these
    RFC 822 defined options. If both -f and -i options are omitted then the
    RFC 821 MAIL FROM statement will be defaulted to use the installation-defined
    default sender address.

     

     

    展开全文
  • blat文件包

    2013-06-20 20:28:04
    blat
  • 可通过blat进批处理发邮件; @echo off cd /d C:\Users\Administrator\Desktop\blat3219\full blat -install smtp.163.com fumacnnb@163.com blat TestMailBody.txt -to 635926522@qq....
  • blat自动发送邮件

    2017-05-06 10:40:53
    Blat 是一个命令行发邮件的小工具,仅支持简单的SMTP协议,需要SMTP服务器的支持。
  • get_BLAT_reads 脚本用于清理NGS读取,BLAT用于引用并提取匹配的读取 由Matt Gitzendanner撰写 佛罗里达大学 get_reads_w_blat_hit_pe.py 该脚本遍历BLAT psl文件(不包含标题,但是如果它们也存在的话,可能会起...
  • 开源的 blat邮件发送

    2016-03-25 11:45:02
    开源的 blat邮件发送
  • 用于UCSC BLAT服务器的Docker容器,带有参考基因组,人类hg19,hg38和鼠标mm10 正在运行的容器 $ sudo docker run -it -p 55519:55519 misshie/ucsc-blat-hg19 $ sudo docker run -it -p 55538:55538 misshie/ucsc-...
  • blat参数详细说明

    2019-04-20 15:48:26
    blat - Standalone BLAT v. 36x2 fast sequence search command line tool usage: blat database query [-ooc=11.ooc] output.psl where: database and query are each either a .fa, .nib or .2bit file, or a list...

    blat - Standalone BLAT v. 36x2 fast sequence search command line tool
    usage:
    blat database query [-ooc=11.ooc] output.psl
    where:
    database and query are each either a .fa, .nib or .2bit file, or a list of these files with one file name per line.
    -ooc=11.ooc tells the program to load over-occurring 11-mers from an external file. This will increase the speed by a factor of 40 in many cases, but is not required.
    output.psl is the name of the output file.
    Subranges of .nib and .2bit files may be specified using the syntax:
    /path/file.nib:seqid:start-end
    or
    /path/file.2bit:seqid:start-end
    or
    /path/file.nib:start-end
    With the second form, a sequence id of file:start-end will be used.
    options:
    -t=type Database type. Type is one of:
    dna - DNA sequence
    prot - protein sequence
    dnax - DNA sequence translated in six frames to protein
    The default is dna.
    -q=type Query type. Type is one of:
    dna - DNA sequence
    rna - RNA sequence
    prot - protein sequence
    dnax - DNA sequence translated in six frames to protein
    rnax - DNA sequence translated in three frames to protein
    The default is dna.
    output.psl is the name of the output file.
    Subranges of .nib and .2bit files may be specified using the syntax:
    /path/file.nib:seqid:start-end
    or
    /path/file.2bit:seqid:start-end
    or
    /path/file.nib:start-end
    With the second form, a sequence id of file:start-end will be used.
    options:
    -t=type Database type. Type is one of:
    dna - DNA sequence
    prot - protein sequence
    dnax - DNA sequence translated in six frames to protein
    The default is dna.
    -q=type Query type. Type is one of:
    dna - DNA sequence
    rna - RNA sequence
    prot - protein sequence
    dnax - DNA sequence translated in six frames to protein
    rnax - DNA sequence translated in three frames to protein
    The default is dna.
    -prot Synonymous with -t=prot -q=prot.
    -ooc=N.ooc Use overused tile file N.ooc. N should correspond to the tileSize.
    -tileSize=N Sets the size of match that triggers an alignment.
    Usually between 8 and 12.
    Default is 11 for DNA and 5 for protein.
    -stepSize=N Spacing between tiles. Default is tileSize.
    -oneOff=N If set to 1, this allows one mismatch in tile and still triggers an alignment. Default is 0.
    -minMatch=N Sets the number of tile matches. Usually set from 2 to 4.
    Default is 2 for nucleotide, 1 for protein.
    -minScore=N Sets minimum score. This is the matches minus the
    mismatches minus some sort of gap penalty. Default is 30.
    -minIdentity=N Sets minimum sequence identity (in percent). Default is
    90 for nucleotide searches, 25 for protein or translated
    protein searches.
    -maxGap=N Sets the size of maximum gap between tiles in a clump. Usually
    set from 0 to 3. Default is 2. Only relevent for minMatch > 1.
    -noHead Suppresses .psl header (so it’s just a tab-separated file).
    -makeOoc=N.ooc Make overused tile file. Target needs to be complete genome.
    -repMatch=N Sets the number of repetitions of a tile allowed before
    -prot Synonymous with -t=prot -q=prot.
    -ooc=N.ooc Use overused tile file N.ooc. N should correspond to
    the tileSize.
    -tileSize=N Sets the size of match that triggers an alignment.
    Usually between 8 and 12.
    Default is 11 for DNA and 5 for protein.
    -stepSize=N Spacing between tiles. Default is tileSize.
    -oneOff=N If set to 1, this allows one mismatch in tile and still
    triggers an alignment. Default is 0.
    -minMatch=N Sets the number of tile matches. Usually set from 2 to 4.
    Default is 2 for nucleotide, 1 for protein.
    -minScore=N Sets minimum score. This is the matches minus the
    mismatches minus some sort of gap penalty. Default is 30.
    -minIdentity=N Sets minimum sequence identity (in percent). Default is
    90 for nucleotide searches, 25 for protein or translated
    protein searches.
    -maxGap=N Sets the size of maximum gap between tiles in a clump. Usually
    set from 0 to 3. Default is 2. Only relevent for minMatch > 1.
    -noHead Suppresses .psl header (so it’s just a tab-separated file).
    -makeOoc=N.ooc Make overused tile file. Target needs to be complete genome.
    -repMatch=N Sets the number of repetitions of a tile allowed before
    it is marked as overused. Typically this is 256 for tileSize
    12, 1024 for tile size 11, 4096 for tile size 10.
    Default is 1024. Typically comes into play only with makeOoc.
    Also affected by stepSize: when stepSize is halved, repMatch is
    doubled to compensate.
    -mask=type Mask out repeats. Alignments won’t be started in masked region
    but may extend through it in nucleotide searches. Masked areas
    are ignored entirely in protein or translated searches. Types are:
    lower - mask out lower-cased sequence
    upper - mask out upper-cased sequence
    out - mask according to database.out RepeatMasker .out file
    file.out - mask database according to RepeatMasker file.out
    -qMask=type Mask out repeats in query sequence. Similar to -mask above, but
    for query rather than target sequence.
    -repeats=type Type is same as mask types above. Repeat bases will not be
    masked in any way, but matches in repeat areas will be reported
    separately from matches in other areas in the psl output.
    -minRepDivergence=NN Minimum percent divergence of repeats to allow
    them to be unmasked. Default is 15. Only relevant for
    masking using RepeatMasker .out files.
    -dots=N Output dot every N sequences to show program’s progress.
    it is marked as overused. Typically this is 256 for tileSize
    12, 1024 for tile size 11, 4096 for tile size 10.
    Default is 1024. Typically comes into play only with makeOoc.
    Also affected by stepSize: when stepSize is halved, repMatch is
    doubled to compensate.
    -mask=type Mask out repeats. Alignments won’t be started in masked region
    but may extend through it in nucleotide searches. Masked areas
    are ignored entirely in protein or translated searches. Types are:
    lower - mask out lower-cased sequence
    upper - mask out upper-cased sequence
    out - mask according to database.out RepeatMasker .out file
    file.out - mask database according to RepeatMasker file.out
    -qMask=type Mask out repeats in query sequence. Similar to -mask above, but
    for query rather than target sequence.
    -repeats=type Type is same as mask types above. Repeat bases will not be
    masked in any way, but matches in repeat areas will be reported
    separately from matches in other areas in the psl output.
    -minRepDivergence=NN Minimum percent divergence of repeats to allow
    them to be unmasked. Default is 15. Only relevant for
    masking using RepeatMasker .out files.
    -dots=N Output dot every N sequences to show program’s progress.
    -trimT Trim leading poly-T.
    -noTrimA Don’t trim trailing poly-A.
    -trimHardA Remove poly-A tail from qSize as well as alignments in
    psl output.
    -fastMap Run for fast DNA/DNA remapping - not allowing introns,
    requiring high %ID. Query sizes must not exceed 5000.
    -out=type Controls output file format. Type is one of:
    psl - Default. Tab-separated format, no sequence
    pslx - Tab-separated format with sequence
    axt - blastz-associated axt format
    maf - multiz-associated maf format
    sim4 - similar to sim4 format
    wublast - similar to wublast format
    blast - similar to NCBI blast format
    blast8- NCBI blast tabular format
    blast9 - NCBI blast tabular format with comments
    -fine For high-quality mRNAs, look harder for small initial and
    terminal exons. Not recommended for ESTs.
    -maxIntron=N Sets maximum intron size. Default is 750000.
    -extendThroughN Allows extension of alignment through large blocks of Ns.

    展开全文
  • Blat(mat)-开源

    2021-04-27 15:27:48
    blat(mat)是用于打印数学的盲文翻译器。 它采用西班牙语的六点数学盲文(不是Nemeth代码)文本,并将其转换为HTML文件,准备通过ASCIIMathML(javascript)转换为XHTML + MathML。
  • blat3222 Blat-Windows命令行SMTP邮件程序 小巧的实用命令行工具。使用方法可参见我的博客 附带批处理命令 https://blog.csdn.net/ilqgffvramusm2864/article/details/106332050
  • 使用Blat发邮件

    千次阅读 2017-04-10 17:06:02
    定时发送邮件相信很多人都...今天我们来介绍一款“短小精悍”的小工具——Blat,来实现这个功能! What is Blat? Blat is a Windows (32 & 64 bit) command line utility that sends eMail using SMTP or post to use

    定时发送邮件相信很多人都遇到过,比如说每天7点整,要把前24小时在网站上产生的数据提交给相应的部门做后期处理。今天我们来介绍一款“短小精悍”的小工具——Blat,来实现这个功能!
    What is Blat?
    Blat is a Windows (32 & 64 bit) command line utility that sends eMail using SMTP or post to usenet using NNTP.

    首先要下载Blat:https://sourceforge.net/projects/blat/files/
    下载后解压缩,cmd进入到当前目录下,敲入如下命令(以163邮箱为例):
    blat -install smtp.163.com admin@163.com
    然后就可以发邮件了,先在当前目录下新建body.txt,在里面写入邮件正文,然后敲入如下命令:
    blat body.txt -to a@163.com,b@163.com -u admin@163.com -pw 123 -subject 主题 -attach D:\PushJobLog\msg_separate\Message.txt
    很明显,-to后面是邮件接受者,多个对象以“,”隔开,-u是发送者,-pw是发送者的密码,-subject是邮件主题,-attach是附件

    以上,就完成了邮件发送的功能,但好像还没实现“定时”,分明是手动执行命令来的嘛,摔!
    不要方,我们现在把命令写到一个bat文件中:
    @echo off
    blat -install smtp.163.com admin@163.com
    blat body.txt -to a@163.com,b@163.com -u admin@163.com -pw 123 -subject 主题 -attach D:\PushJobLog\msg_separate\Message.txt
    pause
    我们把这个bat文件命名为sm.bat,也放到当前目录下,然后用windows的计划任务去定时执行这个bat,这里注意下需要在“起始于”那一栏写上路径:
    这里写图片描述

    以上,就可以实现定时发送的任务啦,记得在计划任务执行前更新body.txt和Message.txt哦。

    但是,每天更新body.txt或者Message.txt,那么之前的内容就被覆盖掉了,怎样能够保存下来呢,其实按道理数据库里应该有以往的发送内容的存档,这边简单介绍几个bat,通过bat来实现备份和打包以及删除。

    以发送txt附件为例,假设每天23时59分59秒,程序会生成一个Message.txt在D:\PushJobLog下,我们只要在sm.bat中@echo off下面加上:
    set “Ymd=%date:~,4%%date:~5,2%%date:~8,2%”
    move D:\PushJobLog\Message.txt D:\PushJobLog\msg_separate\%ymd%.txt
    然后再执行blat发送命令,这样每天都会有一个以日期命名的txt,并且将这个txt发送出去。

    时间长了,日子久了,msg_separate这个文件下就会有越来越多的txt,这时候我想把它们压缩打包,对于那些时间炒鸡久的我们甚至需要删除。
    压缩打包的话我们要借助于WinRAR,新建一个bat文件,命令如下:
    “C:\Program Files\WinRAR\WinRAR.exe” a -df -agYYYYMMDDHHMM D:\Backup\msg_ D:\PushJobLog\msg_separate*.txt
    这个任务会将msg_separate文件夹下所有txt格式的文件打包到D:\Backup下,并以msg_201701101700.rar这种格式命名。(”C:\Program Files\WinRAR\WinRAR.exe”是WinRAR的安装路径)

    删除的话,同样新建一个bat,命令如下:
    set SrcDir=D:\Backup
    set DaysAgo=30
    forfiles /p %SrcDir% /s /m *.rar /d -%DaysAgo% /c “cmd /c del /f /q /a @path”
    这个任务会将D:\Backup下所有30天前的rar文件删除。

    展开全文
  • Blat - Windows命令行SMTP邮件程序-附件资源
  • blat analysis

    千次阅读 2012-07-08 12:28:02
    blat database query [-ooc=11.ooc] output.psl where: database and query are each either a .fa , .nib or .2bit file, or a list these files one file name per line. -ooc=
    usage:
    
       blat database query [-ooc=11.ooc] output.psl
    
    where:
    
       database and query are each either a .fa , .nib or .2bit file,
    
       or a list these files one file name per line.
    
       -ooc=11.ooc tells the program to load over-occurring 11-mers from
    
                   and external file.  This will increase the speed
    
                   by a factor of 40 in many cases, but is not required
    
       output.psl is where to put the output.
    
       Subranges of nib and .2bit files may specified using the syntax:
    
          /path/file.nib:seqid:start-end
    
       or
    
          /path/file.2bit:seqid:start-end
    
       or
    
          /path/file.nib:start-end
    
       With the second form, a sequence id of file:start-end will be used.
    
    options:
    
       -t=type     Database type.  Type is one of:
    
       库序列        dna - DNA sequence
    
                     prot - protein sequence
    
                     dnax - DNA sequence translated in six frames to protein
    
                   The default is dna
    
       -q=type     Query type.  Type is one of:
    
      查询序列       dna - DNA sequence
    
                     rna - RNA sequence
    
                     prot - protein sequence
    
                     dnax - DNA sequence translated in six frames to protein
    
                     rnax - DNA sequence translated in three frames to protein
    
                   The default is dna
    
       -prot       Synonymous with -t=prot -q=prot
    
       -ooc=N.ooc  Use overused tile file N.ooc.  N should correspond to
    
                   the tileSize
    
       -tileSize=N sets the size of match that triggers an alignment.
    
                   Usually between 8 and 12
    
                   Default is 11 for DNA and 5 for protein.
    
       -stepSize=N spacing between tiles. Default is tileSize.
    
       -oneOff=N   If set to 1 this allows one mismatch in tile and still
    
                   triggers an alignments.  Default is 0.
    
       -minMatch=N sets the number of tile matches.  Usually set from 2 to 4
    
                   Default is 2 for nucleotide, 1 for protein.
    
       -minScore=N sets minimum score.  This is the matches minus the
    
                   mismatches minus some sort of gap penalty.  Default is 30
    
       -minIdentity=N Sets minimum sequence identity (in percent).  Default is
    
                   90 for nucleotide searches, 25 for protein or translated
    
                   protein searches.
    
       -maxGap=N   sets the size of maximum gap between tiles in a clump.  Usually
    
                   set from 0 to 3.  Default is 2. Only relevent for minMatch > 1.
    
       -noHead     suppress .psl header (so it's just a tab-separated file)
    
       -makeOoc=N.ooc Make overused tile file. Target needs to be complete genome.
    
       -repMatch=N sets the number of repetitions of a tile allowed before
    
                   it is marked as overused.  Typically this is 256 for tileSize
    
                   12, 1024 for tile size 11, 4096 for tile size 10.
    
                   Default is 1024.  Typically only comes into play with makeOoc.
    
                   Also affected by stepSize. When stepSize is halved repMatch is
    
                   doubled to compensate.
    
       -mask=type  Mask out repeats.  Alignments won't be started in masked region
    
                   but may extend through it in nucleotide searches.  Masked areas
    
                   are ignored entirely in protein or translated searches. Types are
    
                     lower - mask out lower cased sequence
    
                     upper - mask out upper cased sequence
    
                     out   - mask according to database.out RepeatMasker .out file
    
                     file.out - mask database according to RepeatMasker file.out
    
       -qMask=type Mask out repeats in query sequence.  Similar to -mask above but for query rather than target sequence.
    
       -repeats=type Type is same as mask types above.  Repeat bases will not be
    
                   masked in any way, but matches in repeat areas will be reported
    
                   separately from matches in other areas in the psl output.
    
       -minRepDivergence=NN - minimum percent divergence of repeats to allow
    
                   them to be unmasked.  Default is 15.  Only relevant for
    
                   masking using RepeatMasker .out files.
    
       -dots=N     Output dot every N sequences to show program's progress
    
       -trimT      Trim leading poly-T
    
       -noTrimA    Don't trim trailing poly-A
    
       -trimHardA  Remove poly-A tail from qSize as well as alignments in
    
                   psl output
    
       -fastMap    Run for fast DNA/DNA remapping - not allowing introns,
    
                   requiring high %ID
    
       -out=type   Controls output file format.  Type is one of:
    
                       psl - Default.  Tab separated format, no sequence
    
                       pslx - Tab separated format with sequence
    
                       axt - blastz-associated axt format
    
                       maf - multiz-associated maf format
    
                       sim4 - similar to sim4 format
    
                       wublast - similar to wublast format
    
                       blast - similar to NCBI blast format
    
                       blast8- NCBI blast tabular format
    
                       blast9 - NCBI blast tabular format with comments
    
       -fine       For high quality mRNAs look harder for small initial and
    
                   terminal exons.  Not recommended for ESTs
    
       -maxIntron=N  Sets maximum intron size. Default is 750000
    
       -extendThroughN - Allows extension of alignment through large blocks of N's
    


    Blat,全称The BLAST-Like Alignment Tool, 可以称为“类BLAST比对工具”,由W.James Kent于2002年开发。当时随着人类基因组计划的进展,把大量的基因和ESTs快速定位到较大的基因组上称为一种迫切需要。blast相对于这种比对有几个缺陷:速度偏慢、结果难于处理、无法表示包含intron的基因定位。Blat就是再这种形势下应运而生了。

    Blat的主要特点是:速度快,共线性输出结果简单易读。对于比较小的序列(如cDNA等)对大基因组的比对,blat无疑是首选。Blat把相关的呈共线性的比对结果连接成更大的比对结果,从中也可以很容易的找到exons和introns。因此,在相近物种的基因同源性分析和EST分析中,blat得到了广泛的应用。

    如下图所示,blast会把每一个比对作为一个输出,而blat会把一些符合共线性关系的比对连接起来作为一个输出。

    Blat的输入文件必须满足fasta格式,运行时非常的简单,不需要进行建库就可以直接比对。Blat的基本命令:

    blat      database  query [-参数]  output

    程序正常运行时,会在读完database中的所有subject序列时在屏幕输出database的统计结果:

    Loaded 1493629 letters in 486 sequences###486条序列中有1493629个letters

    Searched 1493629 bases in 486 sequences###自己和自己比对

    默认的输出结果是列表形式的文本文件,即psl格式。

    psl格式的结果包含了详细的比对位置信息,每一列的意义都在文件开头列出。第1~8列是通体的比对统计,包括精确比对碱基数、错配、query和subject上的gap个数与gap总长等;第9~17列是比对位置信息,包括比对方向、query和subject的名字、长度、比对起止位置;18~21列是显示每一个精确比对的block的信息,包括blocks数、每个block的长度和在query、subject上的位置。

    对psl输出结果,需要注意一下几点:

    1.blat的结果在subject上允许存在很大的gap(intron区域),所以同一个结果在query和subjects上覆盖的区域可能会相差很多,这一点与blast不同。

    2.在基因对基因组的比对中,block的个数不能等同于exon的个数。因为blat对block的定义是一个没有插入缺失的比对,任何插入或者缺失的碱基都会使一个block终止,所以一个exon很可能是有很多block构成的。因此exon和intron的个数要通过足够大的gap来判断。

    3.psl结果里面碱基位置的计算是从0开始的而不是1.

     

    做不同类型的比对时候需要注意一个问题,就是 “-t”和“-q”的定义必须为同一类型。比如database和query都是蛋白序列,并且两者同时定义为 “prot”的时候,比对能够正常进行;如果database是DNA序列而query序列是蛋白序列,那么在定义 “-q=prot”的同时还需要定义 “-tdnax”.下面就用同一个基因的DNA和蛋白序列举几个例子。

    运行命令1:

    blat  cdna.seq  pro.seq  -q=prot  out.psl

    程序报错退出:

    d  and  q  must both be either protein or dna

    运行命令2:

    blat  cdna.seq  pro.seq  -t=dnax  -q=prot  -noHead  out.psl

    ok, right

    注意蛋白比对和核酸比对在输出上的不同点,在显示方向的位置显示了2个“+”,表示query和subject都是正向比对。

    运行命令3,核酸序列的蛋白级别比对:

    blat  cdna.seq  cdna.seq  -t=dnax  -q=dnax  -noHead out.psl

    展开全文
  • blat命令I was reading my boss's blog today, as he's a hard core GTDpractitioner- more than I - and I'm trying to getbetter at it. 我今天在阅读老板的博客,因为他是GTD的核心从业者-比我更多-并且我正在...
  • Vicente Blat的图片组合 此仓库包含Vicente Blat的个人作品集。
  • windows下命令行发邮件工具 blat_3.26 带文档
  • Blat A Windows 32 & 64 bit command line SMTP mailer Use it to automatically eMail logs the contents of a html FORM or whatever else you need to send Last Update: 2013 12 27 version:312 pc 32
  • 使用RNA转录本评估装配-解析转录组与基因组的BLAT输出 输出如下所示: Percentage of transcripts with a BLAT entry (15661/15752): 0.994222955815135 Total % coverage of all positions (10303278 / 10491059)...
  • blat324_64.full.zip

    2015-03-21 12:54:20
    blat324_64.full.zip windows64位版
  • blat324_32.full.zip

    2015-03-21 12:53:18
    blat324_32.full.zip windows32位版
  • 使用适用于 Windows 的 Blat SMTP 邮件程序从 R 发送电子邮件。 这个包是用于 Windows 的 Blat 的包装器,它支持简单的电子邮件功能。 有关可用功能的详细信息,请参阅。 您需要单独下载 Blat 可执行文件(公共域)...
  • blat 实现bat脚本发送邮件,亲自编写文档,测试好用,含安装包和使用说明文档(内含bat命令); 一、下载和安装 二、bat脚本 三、脚本参数解析 四、其他 。 下载即可,少走弯路、
  • windows blat发送邮件

    千次阅读 2016-01-07 10:22:00
    1,blat install methods: 1) Copy the file "Blat.exe" to your "\WINNT\SYSTEM32" directory, or to  any other directory in your path. 2) Optionaly, run "Blat -install smtp.your...
  • linux 下安装blat软件

    2019-09-25 13:17:09
    blat是一款很经典的比对工具,与blast相比,具有速度快、共线性输出比对结果等优点。但是,blat源码包里面的README文件写得很不清楚,这里,我来提供一份详细的安装文档。 0、下载地址:http://users.soe.ucsc.edu/...
  • 如何从下载 UCSC 的 blatUCSC中的工具blat下载方式blat 问题 UCSC中的工具 http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/. blat下载方式 #For linux rsync -a rsync://hgdownload.soe.ucsc.edu/genome/...
  • 获取程序: http://www.blat.net/ https://sourceforge.net/projects/blat/files/ ...配置Blat的SMTP服务器:blat -install sever usr try port [profile] 163邮箱举例:blat -install smtp.163.com user@163.com...

空空如也

空空如也

1 2 3 4 5 ... 20
收藏数 767
精华内容 306
关键字:

blat