tell me how to unstand this EST display

Dr. Hiranya S. Roychowdhury hroychow at nmsu.edu
Sat Jul 22 15:10:24 EST 2000


Visit the NCBI site ("ncbi.nlm.nih.gov") for explanations and links that
will provide the necessary background for the interpretation of those
terms. They are essentially statistical terms that are hard to explain over
the internet. You may also want to read a few recent articles and books on
Bioinformatics.

At 03:56 PM 7/22/00 +0100, sdyang at china.com wrote:
> I have search this EST from webpage of bioinfo.okstate.edu ,It will be
useful to me .But there are some scientific items I can not know its
meaning ,such as score,expect,positives .I need your kind help .Furthmore
,I hope you can tell how to use EST database to identify a new cDNA .you
may refer me some useful articles which have explain EST more detailed .
>
>Thank you 
>sdyang
>
>Contig contig2000Jan241456_1087 Retrieved Successfully !!! 
>
>
>The Retrieved Contig Data is as follows :
>
>
>Contig Name,No.of one-line Descriptions,Characters In Sequence,Average of
Score in Bits(Max Score,Min Score)
>> contig2000Jan241456_1087!5!700!106.40(110, 101)!
> Sequences Producing Significant Alignments                        Score
E      Identities      Positives
>                                                                 (Bits) Value
>gi|3318617|dbj|BAA31585.1| (AB016066) mitochondrial phosphate transporter
[Arabidopsis                       !110! 1e-23!    52/56 (92%)!    56/56
(99%)!
>gi|3318611|dbj|BAA31582.1| (AB016063) mitochondrial phosphate transporter
[Glycine max]                      !109! 3e-23!    52/56 (92%)!    55/56
(97%)!
>gi|3318613|dbj|BAA31583.1| (AB016064) mitochondrial phosphate transporter
[Zea mays]                         !106! 1e-22!    51/56 (91%)!    54/56
(96%)!
>gi|3318615|dbj|BAA31584.1| (AB016065) mitochondrial phosphate transporter
[Oryza sativa]                     !106! 1e-22!    51/56 (91%)!    54/56
(96%)!
>gi|1842188|emb|CAA69726.1| (Y08499) mitochondrial phosphate translocator
[Betula pendula]                    !101! 8e-21!    48/56 (85%)!    52/56
(92%)!
> Significant Alignments :
> gi|3318617|dbj|BAA31585.1| (AB016066) mitochondrial phosphate transporter
[Arabidopsis            thaliana]
>           Length = 288
>           
> Score =  110 bits (272), Expect = 1e-23
> Identities = 52/56 (92%), Positives = 56/56 (99%)
>Query: 58  LSFLNNAKGATVGDAVKKIGVLGLFTRGLPLRIVMIGTLTGAQWGIYDAFKVFVGL 225
>           +SFLNNAKGATVGDAVKKIG++GLFTRGLPLRIVMIGTLTGAQWG+YDAFKVFVGL
>Sbjct: 214 VSFLNNAKGATVGDAVKKIGMVGLFTRGLPLRIVMIGTLTGAQWGLYDAFKVFVGL 269
>  gi|3318611|dbj|BAA31582.1| (AB016063) mitochondrial phosphate
transporter [Glycine max]            Length = 375
>           
> Score =  109 bits (269), Expect = 3e-23
> Identities = 52/56 (92%), Positives = 55/56 (97%)
>Query: 58  LSFLNNAKGATVGDAVKKIGVLGLFTRGLPLRIVMIGTLTGAQWGIYDAFKVFVGL 225
>           +SFLNNAKGATVGDAVKK+G+ GLFTRGLPLRIVMIGTLTGAQWGIYDAFKVFVGL
>Sbjct: 299 VSFLNNAKGATVGDAVKKLGLWGLFTRGLPLRIVMIGTLTGAQWGIYDAFKVFVGL 354
>  gi|3318613|dbj|BAA31583.1| (AB016064) mitochondrial phosphate
transporter [Zea mays]            Length = 366
>           
> Score =  106 bits (263), Expect = 1e-22
> Identities = 51/56 (91%), Positives = 54/56 (96%)
>Query: 58  LSFLNNAKGATVGDAVKKIGVLGLFTRGLPLRIVMIGTLTGAQWGIYDAFKVFVGL 225
>           +SFLNNAKGATVGDAVKK+G+ GLFTRGLPLRIVMIGTLTGAQWGIYDAFKV VGL
>Sbjct: 291 VSFLNNAKGATVGDAVKKLGLWGLFTRGLPLRIVMIGTLTGAQWGIYDAFKVMVGL 346
>  gi|3318615|dbj|BAA31584.1| (AB016065) mitochondrial phosphate
transporter [Oryza sativa]            Length = 368
>           
> Score =  106 bits (263), Expect = 1e-22
> Identities = 51/56 (91%), Positives = 54/56 (96%)
>Query: 58  LSFLNNAKGATVGDAVKKIGVLGLFTRGLPLRIVMIGTLTGAQWGIYDAFKVFVGL 225
>           +SFLNNAKGATVGDAVKK+G+ GLFTRGLPLRIVMIGTLTGAQWGIYDAFKV VGL
>Sbjct: 292 VSFLNNAKGATVGDAVKKLGLWGLFTRGLPLRIVMIGTLTGAQWGIYDAFKVMVGL 347
>  gi|1842188|emb|CAA69726.1| (Y08499) mitochondrial phosphate translocator
[Betula pendula]            Length = 364
>           
> Score =  101 bits (248), Expect = 8e-21
> Identities = 48/56 (85%), Positives = 52/56 (92%)
>Query: 58  LSFLNNAKGATVGDAVKKIGVLGLFTRGLPLRIVMIGTLTGAQWGIYDAFKVFVGL 225
>           +SFLNNAKGATVGDAVKK+G+LGL TRGLPLRI M+GTLTG QWGIYDAFKV VGL
>Sbjct: 291 VSFLNNAKGATVGDAVKKMGLLGLCTRGLPLRIFMVGTLTGVQWGIYDAFKVSVGL 346
> ssion library, 30 hours NaCl treatment Mesembryanthemum crystallinum cDNA
clone L30-2603 5', mRNA sequenceTCTCTTTCCTCAA Nucleotide Sequence for
Contig contig2000Jan241456_1087 : 
>CAATGCCAAGGGAGCTACTGTTGGTGATGCCGTTAAGAAGATCGGTGTGTTGGGTCTTTTCACTCGTGGACTTCC
TCTCCGTATTGTCATGATTGGTACCCTCACCGGAGCACAATGGGGTATCTATGATGCATTCAAAGTCTTTGTTGGG
CTGCCAACAACTGGTGGTGCTCCTCCTGCTGCTGCCCCTGCTAAGGTATGAAGATATTGACGAATAGAAGAGAATC
ACGGGTTTTGGATATTTGGAAGGAGTGTTAATAAACACCAGGATTTGCTGATATTTTTGCTCACTGGATAGTGGGA
AAACGATAATTTTTGTTTACTTGAGACCATAATTCATAACATTCTGCAATTAGTTCTGATAATACGTTTATGAAGG
ATGGTTTTGTCCTCATCCTTCATTCCTGAAAGCTCCTTCAAAGTACCGTGTTAGATAAATGTAGGACATGGTTTTT
GTTGTTTCTTTTTCGACCCCAACTAGGAACTGGCAACAGGTGATATTGGGGAATCATACTTCGGTTATATTCTTTT
GACAGAGCTATCGTTGCTGTTTAAGTGAAACAACAATTTATTTTTGGCTT
>
>
>----------------------------------------------
>»¶Ó­²Î¼ÓCNNICÓн±µ÷²é,´ó½±µÈ×ÅÄú£¡
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>ÇëͶƱ֧³Ö¹úÖÐÍø!
>http://cww.com/cnnic.html
>
>
>---
>
>
>
Dr. Hiranya Sankar Roychowdhury
Dept. of Molecular Biology	
PO Box 30001 - 3MLS
New Mexico State University
Las Cruces, NM 88003

Lab: (505) 646 4722
Office: (505) 646 8256
hroychow at nmsu.edu


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