vvv

08111773439416

pnumber

470237294857

Our analysis is based on three sources of data: human genomic sequence assemblies (5), human ESTs from the UniGene database (31) and human EST library information. Human genomic assembly sequences (accession no. NT_XXXX) and ‘draft’ BAC clone sequences (accession nos ACXXXX, ALXXXXX) were downloaded from NCBI (ftp://ftp. ncbi.nih.gov/genomes/H_sapiens and ftp://ftp.ncbi.nih.gov/ genbank/gbhtgXX.seq.gz). Human ESTs and library information were downloaded from UniGene (ftp://ftp.ncbi.nih.gov/repository/UniGene). Additional EST library information about human tissue sources was obtained from the NCBI Library Browser, downloaded from www.ncbi.nlm.nih.gov/UniGene/lbrowse.cgi?ORG=Hs. The work described in this paper is based on the January 2002 release of the human genome and UniGene data.

Alignment construction. The goal of the first step is to obtain a set of native EST alignments to the genomic template. After the genomic locus for a RefSeq transcript is identified, the genomic sequence containing the genic region and up to 20 kb extensions at both ends is extracted. This genomic template is searched against dbEST usingWU-BLASTN (Gish 1996–2000) and sequences of high-scoring EST hits are aligned to the genomic template using sim4 (Florea et al. 1998).
2.
Gene structure prediction. In the second step, genomic EST alignments with near-identity are used to infer the exon/intron structures. Although TAP can predict genes simultaneously on both strands, for simplicity we herein describe the gene prediction results with respect to the plus strand for each RefSeq gene. First, the splice pair, donor, and acceptor splice junctions that define the boundaries of an intron, are inferred from segmentation patterns in EST alignments and screened according to splice site patterns. The test set contains 1007 multiexon genes with 8879 pairs of known splice junctions.TAP correctly identified 5111 known splice pairs, yielding a sensitivity of 58%. Separately, PASS scans the genomic sequence for poly-A sites by clustering 3′ ESTs. For 290 RefSeq sequences with known poly-A sites, PASS scored a 84.5% sensitivity. Second, mutually exclusive splicing patterns are resolved by selecting the “predominant” splice pairs, according to EST coverage, and a joint gene structure for the entire genomic region is assembled from individual splice pairs. The EST-based connectivity between two adjacent splice pairs is examined to define exons and to delineate gaps in EST coverage. Finally, the gene boundaries are defined by segmenting the joint gene structure into individual genes at inferred intergenic regions (Fig. 1).
3.
Evaluation. The predicted gene structure are compared with the known gene structures to evaluate the accuracy of TAP. (A Web-based interface to TAP and the reconstruction results for 1124 RefSeq genes are available at http://stl.wustl.edu/∼zkan/TAP/.)

pkgconfig

export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/local/lib/pkgconfig

wf

156151525

visanum

08116273354858

error : did not return a true value

The "did not return a true value" error usually means that a module didn't have a positive value at the end such as the usual "1;".

my own perl package

[xusheng@b82570 UT_script_test]$ PERL5LIB=/home/xusheng/UTScript/
[xusheng@b82570 UT_script_test]$ export PERL5LIB

calling R from Perl

system("R \< script.R");

contact info ABI

Jason smith :  Jason.smith@appliedbiosystems.com

Xiaoying Lin: xiaoyinglin@appliedbiosystems.com

card number

421624512207

SNP in promoter

To identify DNA sequence variants that may represent candidate quantitative trait nucleotides underlying eQTLs, we generated sequence data for the most statistically significant cis-acting eQTL genes. Although variation in all parts of the gene can affect transcript levels, we focus on variation in promoter or cDNA that might directly influence transcriptional activity or mRNA stability.

three circle graph

venn diagram

Spearman correlation coefficient and p value

sub SpearmanCorrelation

{

        my ($Probe1,$Probe2)=@_;

        my $c=Statistics::RankCorrelation->new($probehash{$Probe1},$probehash{$Probe2},sorted=>1);

        $data = $probehash{$Probe1};

        my $corr_value=$c->spearman;

        my $ZValue = 0.5*log((1.0+$corr_value)/(1.0-$corr_value));

        $ZValue = $ZValue*sqrt(@$data-2);

        my $corrPValue = 2.0*(1.0 - pnorm(abs($ZValue)));

        return(\$corr_value,\$corrPValue);

}

Linux append

cat a >> b

it will append the content of a to b.

printer IP

Port name: fac-507-81178

port number: 9100 

My computer

Windows IP Configuration

        Host Name . . . . . . . . . . . . : lightwave

        Primary Dns Suffix  . . . . . . . : 

        Node Type . . . . . . . . . . . . : Hybrid

        IP Routing Enabled. . . . . . . . : No

        WINS Proxy Enabled. . . . . . . . : No

        DNS Suffix Search List. . . . . . : utmem.edu

Ethernet adapter Local Area Connection 2:

        Connection-specific DNS Suffix  . : utmem.edu

        Description . . . . . . . . . . . : Marvell Yukon 88E8053 PCI-E Gigabit Ethernet Controller

        Physical Address. . . . . . . . . : 00-17-F2-D0-01-70

        Dhcp Enabled. . . . . . . . . . . : Yes

        Autoconfiguration Enabled . . . . : Yes

        IP Address. . . . . . . . . . . . : 172.21.163.217

        Subnet Mask . . . . . . . . . . . : 255.255.248.0

        Default Gateway . . . . . . . . . : 172.21.160.1

        DHCP Server . . . . . . . . . . . : 128.169.63.2

        DNS Servers . . . . . . . . . . . : 132.192.1.46

                                            132.192.13.82

        Primary WINS Server . . . . . . . : 128.169.253.147

        Lease Obtained. . . . . . . . . . : 2008年9月29日 12:06:34

        Lease Expires . . . . . . . . . . : 2008年9月29日 12:21:34

New server

172.21.162.205

root + number(6)

cluster command

Node info

      pbsnodes -a             # show status of all nodes       pbsnodes -a nodeNN      # show status of specified node       pbsnodes -l             # list inactive nodes       pbsnodelist             # list status of all nodes (one per line) 

Queue info

      qstat -Q                      # show all queues       qstat -Q               # show status of specified queue       qstat -f -Q            # show full info for specified queue       qstat -q                      # show all queues (alternative format)       qstat -q               # show status of specified queue (alt.) 

Job submission and monitoring

      qsub               # submit to default queue       qsub -q     # submit to specified queue       qsub -l nodes=4:ppn=2    # request 4x2 processors       qsub -l nodes=nodeNN     # run on specified node        qsub -l cput=HH:MM:SS        # limit on CPU time (serial job)       qsub -l walltime=HH:MM:SS    # limit on wallclock time (parallel job)        qdel                  # delete job (with  from qstat)        qstat -a                      # show all jobs       qstat -a               # show all jobs in specified queue               qstat -f              # show full info for specified job       qstat -n                      # show all jobs and the nodes they occupy

Server

132.192.81.226

xusheng

Pass: abbreviation+year

vi command

Cursor control and position

h    Left    
Text Link Ads

Editing
j    Down
k    Up
l (or spacebar)    Right
w    Forward one word
b    Back one word
e    End of word
(    Beginning of current sentence
)    Beginning of next sentence
{    Beginning of current paragraph
}    Beginning of next paragraph
[[    Beginning of current section
]]    Beginning of next section    A    Append to end of current line
0    Start of current line    i    Insert before cursor
$    End of current line    I    Insert at beginning of line
^    First non-white character of current line    o    Open line above cursor
+ or RETURN    First character of next line    O    Open line below cursor
-    First character of previous line    ESC    End of insert mode
n |    character n of current line    Ctrl-I    Insert a tab
H    Top line of current screen    Ctrl-T    Move to next tab position
M    Middle line of current screen    Backspace    Move back one character
L    Last line of current screen    Ctrl-U    Delete current line
nH    n lines after top line of current screen    Ctrl-V    Quote next character
nL    n lines before last line of current screen    Ctrl-W    Move back one word
Ctrl-F    Forward one screen    cw    Change word
Ctrl-B    Back one screen    cc    Change line
Ctrl-D    Down half a screen    C    Change from current position to end of line
Ctrl-U    Up half a screen    dd    Delete current line
Ctrl-E    Display another line at bottom of screen    ndd    Delete n lines
Ctrl-Y    Display another line at top of screen    D    Delete remainer of line
z RETURN    Redraw screen with cursor at top    dw    Delete word
z .    Redraw screen with cursor in middle    d}    Delete rest of paragraph
z -    Redraw screen with cursor at bottom    d^    Delete back to start of line
Ctrl-L    Redraw screen without re-positioning    c/pat    Delete up to first occurance of pattern
Ctrl-R    Redraw screen without re-positioning    dn    Delete up to next occurance of pattern
/text    Search for text (forwards)    dfa    Delete up to and including a on current line
/    Repeat forward search    dta    Delete up to, but not including, a on current line
?text    Search for text (backwards)    dL    Delete up to last line on screen
?    Repeat previous search backwards    dG    Delete to end of file
n    Repeat previous search    J    Join two lines
N    Repeat previous search, but it opposite direction    p    Insert buffer after cursor
/text/+n    Go to line n after text    P    Insert buffer before cursor
?text?-n    Go to line n before text    rx    Replace character with x
%    Find match of current parenthesis, brace, or bracket.    Rtext    Replace text beginning at cursor
Ctrl-G    Display line number of cursor    s    Substitute character
nG    Move cursor to line number n    ns    Substitute n characters
:n    Move cursor to line number n    S    Substitute entire line
G    Move to last line in file    u    Undo last change
          U    Restore current line
Text Link Ads
   x    Delete current cursor position
X    Delete back one character
nX    Delete previous n characters
.    Repeat last change
~    Reverse case
y    Copy current line to new buffer
yy    Copy current line
"xyy    Copy current line into buffer x
"Xd    Delete and append into buffer x
"xp    Put contents of buffer x
y]]    Copy up to next section heading
ye    Copy to end of word
          
File Handling
        
:w    Write file    







:w!    Write file (ignoring warnings)
:w! file    Overwrite file (ignoring warnings)
:wq    Write file and quit
:q    Quit
:q!    Quit (even if changes not saved)
:w file    Write file as file, leaving original untouched
ZZ    Quit, only writing file if changed
:x    Quit, only writing file if changed
:n1,n2w file    Write lines n1 to n2 to file
:n1,n2w >> file    Append lines n1 to n2 to file
:e file2    Edit file2 (current file becomes alternate file)
:e!    Reload file from disk (revert to previous saved version)
:e#    Edit alternate file
%    Display current filename
#    Display alternate filename
:n    Edit next file
:n!    Edit next file (ignoring warnings)
:n files    Specify new list of files
:r file    Insert file after cursor
:r !command    Run command, and insert output after current line

投稿、审稿以及修改稿件时的常用句型

[英文]投稿、审稿以及修改稿件时的常用句型

转自：http://blog.csdn.net/luckydongbin/archive/2007/07/21/1701500.aspx

一、投稿时的 Cover latter
1). Here within enclosed is our paper for consideration to be published on "(Journal name)". The further information about the paper is in the following:
The Title: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
The Authors: XXXXXXXXXX XXXXXXXXXXXX and XXXXXXXXXX
The authors claim that none of the material in the paper has been published or is under consideration for publication elsewhere.
I am the corresponding author and my address and other information is as follows:
Address: Department of XXXXXXXXX,
College of Chemistry and Enviromental Science, Henan Normal University
Xinxiang City, Henan Province, 453007,
P.R.China
E-mail:
Tel: +86-XXX-XXXXXXX
Fax: +86-XXX-XXXXXXX
Thank you very much for consideration!
Sincerely Yours,
Dr. XXX

2). Dear Dr. Defendi ML:
I am sending a manuscript entitled “ ” by – which I should like to submit for possible publication in the journal of - .
Yours sincerely

3). Dear Dr. A:
Enclosed is a manuscript entitled “” by sb, which we are submitting for publication in the journal of - . We have chosen this journal because it deals with - . We believe that sth would be of interest to the journal’s readers.

4). Dear Dr. A:
Please find enclosed for your review an original research article, “” by sb. All authors have read and approve this version of the article, and due care has been taken to ensure the integrity of the work. No part of this paper has published or submitted elsewhere. No conflict of interest exits in the submission of this manuscript, and we have attached to this letter the signed letter granting us permission to use Figure 1 from another source.
We appreciate your consideration of our manuscript, and we look forward to receiving comments from the reviewers.
二、询问有无收到稿件
Dear Editors,
We dispatched our manuscript to your journal on 3 August 2006 but have not, as yet, receive acknowledgement of their safe arrival. We fear that may have been lost and should be grateful if you would let us know whether or not you have received them. If not, we will send our manuscript again. Thank you in advance for your help.

三、询问论文审查回音
Dear Editors，
It is more than 12 weeks since I submitted our manuscript (No: ) for possible publication in your journal. I have not yet received a reply and am wondering whether you have reached a decision. I should appreciated your letting me know what you have decided as soon as possible.

四、关于论文的总体审查意见
1. This is a carefully done study and the findings are of considerable interest. A few minor revision are list below.
2. This is a well-written paper containing interesting results which merit publication. For the benefit of the reader, however, a number of points need clarifying and certain statements require further justification. There are given below.
3. Although these observation are interesting, they are rather limited and do not advance our knowledge of the subject sufficiently to warrant publication in PNAS. We suggest that the authors try submitting their findings to specialist journal such as –
4. Although this paper is good, it would be ever better if some extra data were added.
5. This manuscript is not suitable for publication in the journal of – because the main observation it describe was reported 3 years ago in a reputable journal of - .
6. Please ask someone familiar with English language to help you rewrite this paper. As you will see, I have made some correction at the beginning of the paper where some syntax is not satisfactory.
7. We feel that this potentially interesting study has been marred by an inability to communicate the finding correctly in English and should like to suggest that the authors seek the advice of someone with a good knowledge of English, preferable native speaker.
8. The wording and style of some section, particularly those concerning HPLC, need careful editing. Attention should be paid to the wording of those parts of the Discussion of and Summary which have been underlined.
9. Preliminary experiments only have been done and with exception of that summarized in Table 2, none has been repeated. This is clearly unsatisfactory, particularly when there is so much variation between assays.
10. The condition of incubation are poorly defined. What is the temperature? Were antibody used?

五、给编辑的回信
1. In reply to the referee’s main criticism of paper, it is possible to say that –
One minor point raised by the referee concerns of the extra composition of the reaction mixture in Figure 1. This has now been corrected. Further minor changes had been made on page 3, paragraph 1 (line 3-8) and 2 (line 6-11). These do not affect our interpretation of the result.
2. I have read the referee’s comments very carefully and conclude that the paper has been rejected on the sole grounds that it lake toxicity data. I admit that I did not include a toxicity table in my article although perhaps I should have done. This was for the sake of brevity rather than an error or omission.
3. Thank you for your letter of – and for the referee’s comments concerning our manuscript entitled “”. We have studied their comments carefully and have made correction which we hope meet with their approval.
4. I enclosed a revised manuscript which includes a report of additional experiments done at the referee’s suggestion. You will see that our original findings are confirmed.
5. We are sending the revised manuscript according to the comments of the reviewers. Revised portion are underlined in red.
6. We found the referee’s comments most helpful and have revised the manuscript
7. We are pleased to note the favorable comments of reviewers in their opening sentence.
8. Thank you for your letter. I am very pleased to learn that our manuscript is acceptable for publication in Cancer Research with minor revision.
9. We have therefore completed a further series of experiments, the result of which are summarized in Table 5. From this we conclude that intrinsic factor is not account.
10. We deleted the relevant passage since they are not essential to the contents of the paper.
11. I feel that the reviewer’s comments concerning Figures 1 and 2 result from a misinterpretation of the data.
12. We would have include a non-protein inhibitor in our system, as a control, if one had been available.
13. We prefer to retain the use of Table 4 for reasons that it should be clear from the new paragraph inserted at the end of the Results section.
14. Although reviewer does not consider it is important to measure the temperature of the cells, we consider it essential.
15. The running title has been changed to “”.
16. The Materials and Methods section now includes details for measuring uptake of isotope and assaying hexokinase.
17. The concentration of HAT media (page12 paragraph 2) was incorrectly stated in the original manuscript. This has been rectified. The authors are grateful to the referees for pointing out their error.
18. As suggested by both referees, a discussion of the possibility of laser action on chromosome has been included (page16, paragraph 2).
19. We included a new set of photographs with better definition than those originally submitted and to which a scale has been added.
20. Following the suggestion of the referees, we have redraw Figure 3 and 4.
21. Two further papers, published since our original submission, have been added to the text and Reference section. These are:
22. We should like to thank the referees for their helpful comments and hope that we have now produced a more balance and better account of our work. We trust that the revised manuscript is acceptable for publication.
23. I greatly appreciate both your help and that of the referees concerning improvement to this paper. I hope that the revised manuscript is now suitable for publication.
24. I should like to express my appreciation to you and the referees for suggesting how to improve our paper.
25. I apologize for the delay in revising the manuscript. This was due to our doing an additional experiment, as suggested by referees

P value of spearman

                my $c=Statistics::RankCorrelation->new($probehash{$ProbenameArray[$i]},$probehash{$ProbenameArray[$j]},sorted=>1);

                my $corr_value=$c->spearman;

                my $ZValue = 0.5*log((1.0+$corr_value)/(1.0-$corr_value));

                $ZValue = $ZValue*sqrt(26-3);

                my $corrPValue = 2.0*(1.0 - pnorm(abs($ZValue)));

network description in discussion

Verifying the biological relevance of the recovered networks is difficult, since many interactions between genes are currently unknown.

慎思

万事皆三思而后行

PIN Number

Associate Research PIN number: 20055

Blat command

UCSC Blat command:

~/bin/i386/blat ~/GenomeSequences/WholeGenome/WholeGenome.fa Probeseq.fa ProbeMap.txt -stepSize=5 -minScore=0 -minIdentity=0 &