Biopython/C2/Blast/Khasi - Revision history

Hezekiah2016 at 09:53, 31 May 2018

2018-05-31T09:53:32Z

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Hezekiah2016 at 06:09, 29 May 2018

2018-05-29T06:09:14Z

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Hezekiah2016 at 06:01, 29 May 2018

2018-05-29T06:01:35Z

Hezekiah2016: Created page with "{| Border=1 ! Time ! Narration |- | 00:01 | Welcome to this tutorial on ''' BLAST''' using '''Biopython''' tools. (Ngi pdiang sngewbha ia ph..."

2018-02-02T12:11:15Z

Created page with "{| Border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Welcome to this tutorial on ''' BLAST''' using '''Biopython''' tools. (Ngi pdiang sngewbha ia ph..."

New page

{| Border=1
! <center>Time</center>
! <center>Narration</center>

|-
| 00:01
| Welcome to this tutorial on ''' BLAST''' using '''Biopython''' tools.
(Ngi pdiang sngewbha ia phi sha kane ka tutorial shaphang u ''' BLAST''' da kaba pyndonkam ki tools u '''Biopython''')

|-
| 00:06
| In this tutorial, we will learn: * To '''run''' "BLAST" for the '''query sequence''' using Biopython tools
(Ha kane ka jinghikai , ngin sa nang kumno ban: '''run''' "BLAST" na ka bynta ka '''query sequence''' da kaba pyndonkam ki tools u Biopython.

|-
|00:13
| And, '''parse''' the BLAST output for further analysis.
(Bad, '''parse''' ia u BLAST output ban tip kham bniah .

|-
| 00:17
|To follow this tutorial, you should be familiar with undergraduate Biochemistry or Bioinformatics
(Ban sngewthuh ia kane ka tutorial, phi dei ban long kiba shemphang ha ka undergraduate Biochemistry lane Bioinformatics.

|-
|00:24
|and basic '''Python''' programming.
(Bad ka basic '''Python''' programming.

|-
|00:27
|Refer to the '''Python''' tutorials at the given link.
(Pyndonkam da ka '''Python''' tutorials na ka link ba ai harum.

|-
| 00:31
|To record this tutorial, I am using: * '''Ubuntu''' Operating System version 14.10
(Ban record ia kane ka tutorial, nga pyndonkam da ka: * '''Ubuntu''' Operating System version 14.10

|-
|00:37
| '''Python''' version 2.7.8
('''Python''' version 2.7.8

|-
|00:41
| '''Ipython interpretor''' version 2.3.0
('''Ipython interpretor''' version 2.3.0

|-
|00:46
| '''Biopython''' version 1.64 and * a working Internet connection.
('''Biopython''' version 1.64 bad ka internet ba trei kam.

|-
| 00:52
|'''BLAST''' is the acronym for '''Basic Local Alignment Search Tool.'''
('''BLAST''' ka dei ka acronym jong ka '''Basic Local Alignment Search Tool.'''

|-
|00:57
|It is an '''algorithm''' for comparing '''sequence''' information.
(Ka dei ka '''algorithm''' ban pyniapher ki '''sequence''' information.

|-
| 01:02
|The program compares '''nucleotide''' or '''protein''' sequences to sequences in databases and calculates the statistical significance of matches.
(Kane ka program ka pyniapher ia ki '''nucleotide''' lane '''protein''' sequences sha ki sequences ha ki databases bad khein ia ka statistical significance jong ki matches .

|-
|01:14
| There are two different ways to '''run''' BLAST:
(Ki don artylli ki rukom ban '''run''' ia ka BLAST:

|-
|01:17
|Local '''BLAST''' on your machine or run '''BLAST''' over Internet through NCBI servers.
(Ka Local '''BLAST''' ha ka machine jong phi lane run '''BLAST''' lyngba ka Internet jong ka NCBI servers.

|-
| 01:24
|Running '''BLAST''' in '''Biopython''' has two steps.
(Ki don ar tylli ki rukom ban pyndonkam ia ka '''BLAST''' ha ka '''Biopython'''

|-
|01:28
|First, run '''BLAST''' for your '''query sequence''' and get some output.
(Nyngkong, run '''BLAST''' na ka bynta ka '''query sequence''' jong phi bad phin sa ioh output.

|-
|01:33
|Second, '''parse''' the '''BLAST''' output for further analysis.
(Ba ar, '''parse''' ka '''BLAST''' output na ka bynta ka jingkdew ba kham bniah hadien.

|-
| 01:38
|We will open the '''terminal''' and run '''BLAST''' for a nucleotide sequence.
(Ngin sa plie ia ka '''terminal''' bad run '''BLAST''' na ka bynta ka nucleotide sequence.

|-
|01:43
|Open the terminal by pressing '''Ctrl, Alt''' and '''T''' keys simultaneously.
(Plie ia ka terminal da kaba nion sah ia '''Ctrl, Alt''' bad '''T''' keys.

|-
| 01:48
|At the '''prompt''', type: '''ipython''' and press '''Enter'''.
(Ha ka '''prompt''', type: '''ipython''' bad nion '''Enter'''.

|-
| 01:52
|In this tutorial, I will demonstrate how to run '''BLAST''' over internet using '''NCBI BLAST''' service.
(Ha kane ka tutorial, ngan sa pyni kumno ban run ia ka '''BLAST''' lyngba ka internet da kaba pyndonkam da ka '''NCBI BLAST''' service.

|-
|02:01
|Type the following at the prompt: '''from Bio.Blast Import NCBIWWW''' Press '''Enter'''.
(Type kumne harum ha ka prompt: '''from Bio.Blast Import NCBIWWW''' Nion '''Enter'''.

|-
| 02:14
|Next, to '''run''' the BLAST over internet, type the following at the prompt.result= NCBIWWW.qblast("blastn","nt","186429").
(Hadien , ban '''run''' ia u BLAST lyngba ka internet, type ia kaba bud ha ka prompt.result= NCBIWWW.qblast("blastn","nt","186429").

|-
|02:20
|We will use '''qblast function '''in the '''NCBIWWW '''module.
(Ngin pyndonkam da ka '''qblast function ''' ha ka '''NCBIWWW '''module.

|-
| 02:25
|'''qblast function''' takes three '''arguments''':
('''qblast function''' ka shim lai tylli ki '''arguments''':

|-
|02:29
|The first '''argument''' is the '''blast program''' to use for the search.
(Ka '''argument''' ba nyngkong ka dei ka '''blast program''' ba pyndonkam haba wad.

|-
|02:33
|Second, specifies the databases to search against.
(Ba ar, ka pyntikna ia ka databases ban wad pyrshah.

|-
|02:38
|The third '''argument''' is your '''query sequence.'''
(Ka '''argument''' ba lai ka dei ka '''query sequence.''' jong phi

|-
| 02:43
| The input for the '''query sequence''' can be in the form of '''GI''' number or a '''FASTA''' file. Or, it can also be a '''sequence record object'''.
(Ka input jong ka '''query sequence''' ka lah ban dei ha ka rukon jong ka '''GI''' number lane ka '''FASTA''' file. Lane, ka lah ban dei ka '''sequence record object'''.

|-
| 02:53
| For this demonstration, I am using the '''GI number''' for a '''nucleotide sequence'''.
(Na ka bynta kane ka jingpyni, nga pyndonkam ia ka '''GI number''' na ka bynta ka '''nucleotide sequence'''.

|-
|02:58
|The '''GI number''' is for a '''nucleotide sequence''' of '''insulin'''.
(Ka '''GI number''' ka dei na ka bynta ka '''nucleotide sequence''' jong ka '''insulin'''

|-
| 03:03
|The '''qblast function''' also takes a number of other option arguments.
(Ka '''qblast function''' ka shim ruh ia kiwei ki jait option arguments .

|-
|03:09
|These arguments are analogous to the different parameters you can set on the '''BLAST''' web page.
(Kine ki arguments ki long kiba syrïem ha ki parameters bapher bapher ba phi lah ban buh ha ka '''BLAST''' web page.

|-
|03:15
|The '''qblast function''' will return the '''BLAST''' results in '''xml''' format.
(Ka '''qblast function''' kan pynphai ia ka '''BLAST''' results ha ka '''xml''' format.

|-
| 03:20
|Back to the '''terminal'''.
(To ngin ia phai biang sha ka '''terminal'''.

|-
|03:22
|We have to use the appropriate '''Blast''' program,
(Ngi hap ban pyndonkam da ka '''Blast''' program, ba tikna.

|-
|03:25
|depending on whether our query sequence is a '''nucleotide''' or '''protein sequence'''.
(ka shong ruh lada ka query sequence jong ngi ka dei ka '''nucleotide''' lane '''protein sequence'''.

|-
|03:30
|Since our query is a '''nucleotide''', we will use '''blastn '''program and "nt" refers to the '''nucleotide''' database.
(Katba ka query jong ngi ka dei ka '''nucleotide''', ngin pyndonkam ka '''blastn '''program bad "nt" jong ka '''nucleotide''' database.

|-
|03:39
|Details about this are available at the '''NCBI BLAST''' webpage.
(Ki jingtip ba kham bniah jong kine lah ban ioh na '''NCBI BLAST''' webpage.

|-
| 03:45
|The '''blast output''' is stored in the variable '''result''', in the form of an '''xml''' file.
(Ia ka '''blast output''' la buh ha ka variable '''result''', ha ka rukom jong ka '''xml''' file.

|-
|03:51
|Press '''Enter'''.
(Nion '''Enter'''.

|-
| 03:53
| Depending upon the speed of your Internet, it may take a few minutes to complete the '''BLAST''' search.
(Ka shong ha ka jingstet jong ka internet jong ngi ban pyndep ia ka jingwad jong ka '''BLAST'''

|-
| 03:59
| It is important to save the '''xml''' file on the disk before processing further.
(Ka long ruh kaba donkam ban save ia ka '''xml''' file ha ka disk shuwa ban iaid shakhmat.

|-
|04:05
|Type the following lines to '''save''' the '''xml file. '''
(Type ia ki line ba bud ban'''save''' iaka '''xml file. '''

|-
|04:09
|These lines of code will save the search result as '''blast.xml''' in the '''home''' folder.
(Kine ki lines jong ki code kin sa save ia ka jingwad kum '''blast.xml''' ha ka '''home''' folder.

|-
| 04:18
| Navigate to your '''home''' folder and locate the file.
(Phai sha ka '''home''' folder jong ngi bad wad ia ka file.

|-
|04:21
|Click on the file and check the contents of the file.
(Click ha ka file bad check ia ka contents (jingdon) jong ka file.

|-
| 04:30
| Use the code shown in this text file, if you want to use a '''FASTA''' file as a '''query'''.
(Pyndonkam ia u code ba pyni ha kane ka text file, lada phi kwah ban pyndonkam ia u '''FASTA''' file kum u '''query'''.

|-
| 04:36
| Here is the code, if you want to use '''sequence record object''' from a '''FASTA''' file as a query.
(Hangne u don u code, lada phi kwah ban pyndonkam ia ka '''sequence record object''' na ka '''FASTA''' file kum ka query.
|-
| 04:42
|Back to the '''terminal'''.
(To ngin ia phai biang sha ka '''terminal'''.

|-
|04:44
|The next step is to '''parse''' the file to '''extract''' data.
(Ka bynta ba bud ka dei ban '''parse''' ia ka file sha ka '''extract''' data.

|-
|04:48
|The first step in parsing is to open the '''xml''' file for input.
(Ka bynta ba nyngkong jong ka parsing ka dei ban plie ia ka '''xml''' file na ka bynta ka input.

|-
|04:53
|Type the following at the prompt. Press '''Enter'''.
(Type kumne harum ha ka prompt. Nion '''Enter'''.

|-
| 04:57
|Next, '''import''' the module '''NCBIXML''' from "Bio.Blast" '''package'''.
(Hadien , '''import''' ia ka module '''NCBIXML''' na "Bio.Blast" '''package'''.

|-
|05:05
|Press '''Enter'''.
(Nion '''Enter'''.

|-
| 05:07
|Type the following lines to '''parse''' the '''Blast''' output.
(Type ia ki lines ba bud sha ka '''parse''' ia ka '''Blast''' output.

|-
|05:11
|A BLAST '''record''' contains all the information you want to '''extract''' from the '''BLAST''' output.
(Ka BLAST '''record''' ka don ia baroh ki jingpyntip ba phi kwah ban '''extract''' na ka '''BLAST''' output.

|-
| 05:18
|Let us print out some information about all the '''hit'''s in our '''blast report''' greater than a particular threshold.
(To ngin ia print khyndiat ia ki jingpyntip shaphang baroh ki '''hit'''s ha ki '''blast report''' jong ngi kiba kham heh ban ha ki jaka ba ki mih.

|-
|05:27
|Type the following code.
(Type ia u code harum.

|-
|05:30
|For a '''match''' to be significant, expect '''score''' should be less than 0.01.
(Khnang ba ka '''match''' kan long kaba tikna, peit ba u '''score''' u dei ban rit ia ka 0.01.

|-
| 05:37
| For each '''hsp''', that is, high scoring pair, we get the '''title, length, hsp score, gaps''' and '''expect value'''.
(Na ka bynta uwei pa uwei u '''hsp''', kata ka mut, ki shijur ba heh score, ngi ioh ia ka '''title, length, hsp score, gaps''' bad '''expect value'''.

|-
|05:49
|We will also print '''string'''s containing the '''query''', the aligned database sequence and string specifying the match and mismatch positions.
(Ngin ia print ruh ia u '''string'''s uba don ia ka '''query''', ka database sequence ba la pynbeit bad u string ba pyntikna ia ka jingiadei bad jingbymiadei ki positions.

|-
|06:02
|Press '''Enter''' key twice to get the output.
(Nion ia u '''Enter''' key arsien ban ioh ia ka output.

|-
| 06:05
| Observe the output.
(Peit ia ka output.

|-
|06:09
|For each alignment, we have '''length, score, gaps, evalue''' and '''strings'''.
(Na ka bynta kawei pa kawei ka alignment, ngi don '''length, score, gaps, evalue''' bad '''strings'''.

|-
| 06:16
|You can extract the required information using other '''functions''', available in '''Bio.Blast''' package.
(Phi lah ban ioh ia ki jingpyntip ba donkam da kaba pyndonkam kiwei ki '''functions''', ki ba don ha '''Bio.Blast''' package.

|-
|06:24
|We have come to the end of this tutorial.
(Ngi lah poi sha kaba kut jong kane ka tutorial.

|-
| 06:26
| Let's summarize. In this tutorial, we have learnt to run '''BLAST''' for the query nucleotide sequence using '''GI''' number.
(To ngin ia khmih ia kaei kaba ngi lah leh haneng . Ha kane ka tutorial, ngi lah tip kumno ban run ia ka '''BLAST''' na ka bynta ka query nucleotide sequence da kaba pyndonkam da u '''GI''' number.

|-
|06:36
|And, parse the '''BLAST''' output using '''Bio.Blast.Record''' module.
(Bad, ban parse ia u '''BLAST''' output da kaba pyndonkam da ka '''Bio.Blast.Record''' module.

|-
| 06:43
| For the assignment, run''' BLAST Search''' for a '''protein''' sequence of your choice.
(Na ka bynta ka assignment, run ''' BLAST Search''' na ka bynta ka '''protein''' sequence kaba ngi kwah.

|-
|06:50
|'''Save''' the output file and parse the data contained in the file.
('''Save''' ia ka output file bad parse ia ka data kaba don ha ka file.

|-
|06:55
|Your completed assignment should have the following lines of code, as shown in this file.
(Ka assignment ba lah dep jong phi ka dei ban don ia ki lines ba don code , kumba lah pyni ha kane ka file.

|-
|07:01
|Observe the code. Since our '''query''' is '''protein''' sequence, we have used '''blastp '''program and "nr", that is, non-redundant protein database for the '''BLAST''' search.
(Peit ia u code. Katba ka '''query''' jong ngi ka dei '''protein''' sequence, ngi lah pyndonkam '''blastp '''program and "nr", kata ka mut, ka protein database kaba donkam na ka bynta ka '''BLAST''' search.

|-
| 07:16
| The video at the following link summarizes the Spoken Tutorial project.
(Ka video kaba don ha ka link ba bud ka batai shai shaphang ka Spoken Tutorial project.

|-
|07:20
|Please download and watch it.
(Sngewbha download bad peit ia ka.

|-
| 07:22
| The Spoken Tutorial Project team conducts workshops and gives certificates for those who pass an online test.
(Ka Spoken Tutorial Project team ka ju pynlong ia ki workshops bad ai ruh ki certificates ia kito kiba pass ia ka online test.

|-
|07:30
|For more details, please write to us.
(Na ka bynta ka jingtip ba kham bniah, sngewbha thoh sha ngi.

|-
| 07:33
| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
(Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Government of India.

|-
|07:40
|More information on this mission is available at the link shown.
(Ki jingtip ba kham pura ia kane ka mission lah ban ioh na link harum.

|-
| 07:45
| This is Snehalatha from '''IIT Bombay''' signing off. Thank you for joining.
(Nga dei ka Snehalatha na '''IIT Bombay'''signing off. Khublei shibun .
|}

@@ Line 5: / Line 5: @@
 |-
 | 00:01
-| Welcome to this tutorial on ''' BLAST''' using '''Biopython''' tools.
+| Ngi pdiang sngewbha ia phi sha kane ka tutorial shaphang u  ''' BLAST''' da kaba pyndonkam ki tools u '''Biopython'''
-(Ngi pdiang sngewbha ia phi sha kane ka tutorial shaphang u  ''' BLAST''' da kaba pyndonkam ki tools u '''Biopython''')
 |-
 | 00:06
-| In this tutorial, we will learn: * To '''run''' "BLAST" for the '''query sequence''' using Biopython tools
+| Ha kane ka jinghikai , ngin sa nang kumno  ban: '''run''' "BLAST" na ka bynta ka '''query sequence''' da kaba pyndonkam ki tools u Biopython.
-(Ha kane ka jinghikai , ngin sa nang kumno  ban: '''run''' "BLAST" na ka bynta ka '''query sequence''' da kaba pyndonkam ki tools u Biopython.
 |-
 |00:13
-| And, '''parse''' the BLAST output for further analysis.
+| Bad, '''parse''' ia u BLAST output ban tip kham bniah .
-(Bad, '''parse''' ia u BLAST output ban tip kham bniah .
 |-
 | 00:17
-|To follow this tutorial, you should be familiar with undergraduate Biochemistry or Bioinformatics
+| Ban sngewthuh  ia kane ka tutorial, phi dei ban long kiba shemphang ha ka  undergraduate Biochemistry lane Bioinformatics.
-(Ban sngewthuh  ia kane ka tutorial, phi dei ban long kiba shemphang ha ka  undergraduate Biochemistry lane Bioinformatics.
 |-
-|00:24
+| 00:24
-|and basic '''Python''' programming.
+| Bad ka basic '''Python''' programming.
-(Bad ka basic '''Python''' programming.
 |-
 |00:27
-|Refer to the '''Python''' tutorials at the given link.
+|Pyndonkam da  ka '''Python''' tutorials na ka link ba ai harum.
-(Pyndonkam da  ka '''Python''' tutorials na ka link ba ai harum.
 |-
 | 00:31
-|To record this tutorial, I am using: * '''Ubuntu''' Operating System version 14.10
+|Ban record ia kane ka tutorial, nga pyndonkam da ka: * '''Ubuntu''' Operating System version 14.10
-(Ban record ia kane ka tutorial, nga pyndonkam da ka: * '''Ubuntu''' Operating System version 14.10
 |-
@@ Line 46: / Line 39: @@
 |00:41
 | '''Ipython interpretor''' version 2.3.0
 |-
 |00:46
-| '''Biopython''' version 1.64 and * a working Internet connection.
+| '''Biopython''' version 1.64 bad ka internet ba trei kam.
-('''Biopython''' version 1.64 bad ka internet ba trei kam.
 |-
 | 00:52
-|'''BLAST''' is the acronym for '''Basic Local Alignment Search Tool.'''
+|'''BLAST''' ka dei ka acronym  jong ka '''Basic Local Alignment Search Tool.'''
-('''BLAST''' ka dei ka acronym  jong ka '''Basic Local Alignment Search Tool.'''
 |-
 |00:57
-|It is an '''algorithm''' for comparing '''sequence''' information.
+|Ka dei ka '''algorithm''' ban pyniapher  ki '''sequence''' information.
-(Ka dei ka '''algorithm''' ban pyniapher  ki '''sequence''' information.
 |-
 | 01:02
-|The program compares '''nucleotide''' or '''protein''' sequences to sequences in databases  and calculates the statistical significance of matches.
+|Kane ka program ka pyniapher  ia ki '''nucleotide''' lane '''protein''' sequences sha ki sequences ha ki databases bad khein ia ka statistical significance jong ki matches .
-(Kane ka program ka pyniapher  ia ki '''nucleotide''' lane '''protein''' sequences sha ki sequences ha ki databases bad khein ia ka statistical significance jong ki matches .
 |-
 |01:14
-| There are two different ways to '''run''' BLAST:
+| Ki don artylli ki rukom ban '''run''' ia ka BLAST:
-(Ki don artylli ki rukom ban '''run''' ia ka BLAST:
 |-
 |01:17
-|Local '''BLAST''' on your machine or run '''BLAST''' over Internet through NCBI servers.
+|Ka Local '''BLAST''' ha ka machine jong phi lane run '''BLAST''' lyngba ka Internet jong  ka NCBI servers.
-(Ka Local '''BLAST''' ha ka machine jong phi lane run '''BLAST''' lyngba ka Internet jong  ka NCBI servers.
 |-
 | 01:24
-|Running '''BLAST''' in '''Biopython''' has two steps.
+|Ki don ar tylli ki rukom ban pyndonkam  ia ka '''BLAST''' ha ka '''Biopython'''
-(Ki don ar tylli ki rukom ban pyndonkam  ia ka '''BLAST''' ha ka '''Biopython'''
 |-
 |01:28
-|First, run '''BLAST''' for your '''query sequence''' and get some output.
+|Nyngkong, run  '''BLAST''' na ka bynta ka '''query sequence''' jong phi bad phin sa ioh  output.
-(Nyngkong, run  '''BLAST''' na ka bynta ka '''query sequence''' jong phi bad phin sa ioh  output.
 |-
 |01:33
-|Second, '''parse''' the '''BLAST''' output for further analysis.
+|Ba ar, '''parse''' ka '''BLAST''' output na ka bynta ka jingkdew  ba kham bniah hadien.
-(Ba ar, '''parse''' ka '''BLAST''' output na ka bynta ka jingkdew  ba kham bniah hadien.
 |-
 | 01:38
-|We will open the '''terminal''' and run '''BLAST''' for a nucleotide sequence.
+|Ngin sa  plie ia ka '''terminal''' bad run '''BLAST''' na ka bynta ka nucleotide sequence.
-(Ngin sa  plie ia ka '''terminal''' bad run '''BLAST''' na ka bynta ka nucleotide sequence.
 |-
 |01:43
-|Open the terminal by pressing '''Ctrl, Alt''' and '''T''' keys simultaneously.
+|Plie ia ka terminal da kaba nion sah  ia '''Ctrl, Alt''' bad '''T''' keys.
-(Plie ia ka terminal da kaba nion sah  ia '''Ctrl, Alt''' bad '''T''' keys.
 |-
 | 01:48
-|At the '''prompt''', type: '''ipython''' and press '''Enter'''.
+|Ha ka '''prompt''', type: '''ipython''' bad nion '''Enter'''.
-(Ha ka '''prompt''', type: '''ipython''' bad nion '''Enter'''.
 |-
 | 01:52
-|In this tutorial, I will demonstrate how to run '''BLAST''' over internet using '''NCBI BLAST''' service.
+|Ha kane ka tutorial, ngan sa pyni kumno ban run ia ka '''BLAST''' lyngba ka internet da kaba pyndonkam da  ka '''NCBI BLAST''' service.
-(Ha kane ka tutorial, ngan sa pyni kumno ban run ia ka '''BLAST''' lyngba ka internet da kaba pyndonkam da  ka '''NCBI BLAST''' service.
 |-
 |02:01
-|Type the following at the prompt: '''from Bio.Blast Import NCBIWWW''' Press '''Enter'''.
+|Type kumne harum ha ka prompt: '''from Bio.Blast Import NCBIWWW''' Nion '''Enter'''.
-(Type kumne harum ha ka prompt: '''from Bio.Blast Import NCBIWWW''' Nion '''Enter'''.
 |-